TANK-BINDING KINASE-1 PROTACs AND ASSOCIATED METHODS OF USE

ABSTRACT

The present invention relates to bifunctional compounds, which find utility to degrade and (inhibit) TBK1. In particular, the present invention is directed to compounds, which contain on one end an E3 ubiquitin ligase binding moiety which binds to an E3 ubiquitin ligase and on the other end a moiety which binds TBK1 such that TBK1 is placed in proximity to the ubiquitin ligase to effect degradation (and inhibition) of TBK1. The present invention exhibits a broad range of pharmacological activities associated with compounds according to the present invention, consistent with the degradation/inhibition of TBK1.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present disclosure is a Divisional Application of U.S. patentapplication Ser. No. 16/284,790, filed 25 Feb. 2019, titled:TANK-BINDING KINASE-1 PROTACs AND ASSOCIATED METHODS OF USE, which is aContinuation Application of U.S. patent application Ser. No. 15/574,770,filed 16 Nov. 2017, titled: TANK-BINDING KINASE-1 PROTACs AND ASSOCIATEDMETHODS OF USE, which is a National Stage of PCT/US2016/036036, filed 6Jun. 2016, titled TANK-BINDING KINASE-1 PROTACs AND ASSOCIATED METHODSOF USE, and which claims priority to the U.S. Provisional ApplicationNo. 62/171,299, filed 5 Jun. 2015, all of which are incorporated hereinby reference in their entirety for all purposes.

BACKGROUND 1. Field of the Discovery

The description provides bifunctional compounds and associated methodsof use. The bifunctional compounds are useful as modulators of targetedubiquitination, especially with respect to a variety of polypeptides andother proteins, which are degraded and/or otherwise inhibited bybifunctional compounds according to the present invention.

2. Background Information

The most common therapeutic interventions available to the prescribingphysician are inhibitor-based drugs such that the active pharmaceuticalingredient mediates the function of the aberrant protein via direct orallosteric inhibition of the mechanistic activity of said protein.

Although inhibition of protein activity is a clinically validatedapproach there are significant constraints to its wider applicability.Firstly, it carries the burden of requiring protracted target engagementfor the mechanism and consequential function to be effectivelyabrogated. Many protein-small molecule interactions are associated withrapid off-rates, resulting in very low inhibitor occupancy of theprotein active site and inadequate downregulation of downstreamsignaling.

Secondly, inability to reach tolerated free-drug concentrations at orabove the in vitro IC₉₀, either because of high plasma protein binding,poor pharmacokinetics, or toxicity can limit the effectiveness ofinhibitor drugs.

Finally, many proteins possess little or no mechanistic activity, yetexecute their biological role by providing a scaffolding function. As aresult, these proteins are less susceptible to the inhibitor paradigm.

E3 ubiquitin ligases (of which hundreds are known in humans) confersubstrate specificity for ubiquitination, and therefore, are moreattractive therapeutic targets than general proteasome inhibitors due totheir specificity for certain protein substrates. The development ofligands of E3 ligases has proven challenging, in part due to the factthat they must disrupt protein-protein interactions. However, recentdevelopments have provided specific ligands which bind to these ligases.For example, since the discovery of nutlins, the first small molecule E3ligase inhibitors, additional compounds have been reported that targetE3 ligases but the field remains underdeveloped.

Technologies that can reduce levels of a target protein in a manner thatrequires only transient interactions with the protein could providesignificant therapeutic utility.

SUMMARY

Proteolysis Targeting Chimeras (PROTACs) (Corson, T. W.; Aberle, N.;Crews, C. M. ACS Chem. Biol. 2008 3(11) 677-692; Sakamoto, K. M.; Kim,K. B.; Verma, R.; Ransick, A.; Stein, B.; Crews, C. M.; Deshaies, R. J.Mol. Cell. Proteomics 2003 2(12) 1350-1358; Sakamoto, K. M.; Kim, K. B.;Kumagai, A.; Mercurio, F.; Crews, C. M.; Deshaies, R. J. Proc. Natl.Acad. Sci. USA 2001 98(15) 8554-8559) are a class of bifunctionalmolecules that live in the “beyond rule of 5” (bRo5) (Barbie, D. A.;Tamayo, P.; Boehm, J. S.; Kim, S. Y.; Moody, S. E.; Dunn, I. F.;Schinzel, A. C.; Sandy, P.; Meylan, E.; Scholl, C.; et al. Nature 2009462 108-112) space that hijack the endogenous protein homeostasismachinery via recruitment of an E3 ubiquitin ligase via one componentligand and associating it with a target protein of interest (PoI)through another component ligand to mediate ubiquitin transfer to, anddegradation of, the latter via the proteasome (FIG. 1).

The present disclosure describes compounds, including compositionscomprising the same, which function to recruit endogenous proteins to anE3 ubiquitin ligase enzyme, e.g., Von Hippel-Lindau (VHL) E3 ubiquitinligase, cereblon, IAP (XIAP), and MDM2, for ubiquitination andsubsequent degradation, and methods of using the same. In particular,the present disclosure provides bifunctional or proteolysis targetingchimeric (PROTAC) compounds, which find utility as modulators oftargeted ubiquitination and degradation of TANK-binding kinase 1 (TBK1).

Thus, in one aspect, the disclosure provides compounds which function torecruit endogenous proteins, e.g., TBK1 proteins, to E3 Ubiquitin Ligasefor ubiquitination and degradation. In certain embodiments, thecompounds have the following general structure:

TBM−L-ULM  (I),

wherein TBM is an TBK1 binding moiety, ULM is an E3 ligase bindingmoiety, e.g., a VHL E3 ligase binding moiety (VLM), cereblon bindingmoiety (CLM), XIAP binding moiety, or MDM2 binding moiety, and L is abond or a linker moiety which links the TBM and ULM.

As such, in certain embodiments, the description provides compoundshaving the following general structure:

TBM−L-VLM  (II),

wherein TBM is an TBK1 binding moiety, VLM is a VHL E3 ligase bindingmoiety and L is a bond or a linker moiety which links the TBM and VLM.

It will be understood that the general structures are exemplary and therespective moieties can be arranged spatially in any desired order orconfiguration, e.g., ULM-L-TBM, and VLM-L-TBM respectively.

In certain additional embodiments, the compounds comprise a plurality ofE3 ligase binding moieties and/or a plurality of TBMs.

In certain embodiments, the description provides a bifunctional compoundhaving a structure as described herein, a salt, a polymorph, and aprodrug thereof.

In another aspect, the description provides compositions comprisingcompounds as described herein, and a pharmaceutically acceptablecarrier. In certain embodiments, the compositions are therapeutic orpharmaceutical compositions comprising an effective amount of a compoundas described herein and a pharmaceutically acceptable carrier. Incertain embodiments, the therapeutic or pharmaceutical compositionscomprise an additional biologically active agent, e.g., an agenteffective for the treatment of cancer.

In any of the aspects or embodiments described herein, the therapeuticcompositions comprising compounds described herein can be in anysuitable dosage form, e.g., solid, or liquid, and configured to bedelivered by any suitable route, e.g., oral, parenteral, intravenous,intraperitoneal, subcutaneous, intramuscular, etc.

In another aspect, the disclosure provides methods of modulating proteinubiquitination and degradation in a subject, e.g., a cell, a tissue,mammal, or human patient, the method comprising administering aneffective amount of a compound as described herein or a compositioncomprising an effective amount of the same to a subject, wherein thecompound or composition comprising the same is effective in modulatingprotein ubiquitination and degradation of the protein in the subject. Incertain embodiments, the protein is TBK1.

In another aspect, the disclosure provides methods of modulating TBK1protein ubiquitination and degradation in a subject, e.g., a cell, atissue, mammal, or human patient, the method comprising administering aneffective amount of a compound as described herein or a compositioncomprising an effective amount of the same to a subject, wherein thecompound or composition comprising the same is effective in modulatingTBK1 protein ubiquitination and degradation of the protein in thesubject.

In another aspect, the disclosure provides methods of treating orameliorating a symptom of a disease related to TBK1 activity in asubject, e.g., a cell, a tissue, mammal, or human patient, the methodcomprising administering an effective amount of a compound as describedherein or a composition comprising an effective amount of the same to asubject in need thereof, wherein the compound or composition comprisingthe same is effective in treating or ameliorating a symptom of a diseaserelated to TBK1 activity in the subject. In a preferred embodiment, thesubject is a human.

In another aspect, the disclosure provides methods for identifying theeffects of the degradation of proteins of interest in a biologicalsystem using compounds according to the present invention.

In another aspect, the description provides kits comprising compounds orcompositions as described herein. The kit may be promoted, distributed,or sold as a unit for performing the methods of the present invention.In addition, the kits of the present invention may preferably containinstructions which describe a suitable use. Such kits can beconveniently used, e.g., in clinical settings, to treat patients.

Where applicable or not specifically disclaimed, any one of theembodiments described herein are contemplated to be able to combine withany other one or more embodiments, even though the embodiments aredescribed under different aspects of the invention. As such, thepreceding general areas of utility are given by way of example only andare not intended to be limiting on the scope of the present disclosureand appended claims. Additional objects and advantages associated withthe compositions, methods, and processes of the present invention willbe appreciated by one of ordinary skill in the art in light of theinstant claims, description, and examples. For example, the variousaspects and embodiments of the invention may be utilized in numerouscombinations, all of which are expressly contemplated by the presentdescription. These additional advantages objects and embodiments areexpressly included within the scope of the present invention. Thepublications and other materials used herein to illuminate thebackground of the invention, and in particular cases, to provideadditional details respecting the practice, are incorporated byreference.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated into and form a partof the specification, illustrate several embodiments of the presentinvention and, together with the description, serve to explain theprinciples of the invention. The drawings are only for the purpose ofillustrating an embodiment of the invention and are not to be construedas limiting the invention. Further objects, features and advantages ofthe invention will become apparent from the following detaileddescription taken in conjunction with the accompanying figures showingillustrative embodiments of the invention, in which:

FIG. 1. Proteolysis Targeting Chimeras (PROTACs) recruit an E3 ligase toa target protein to facilitate ubiquitin transfer from the former to thelatter;

FIG. 2. TBK1 ligand 1 and VHL ligand 2 components selected for inclusioninto the TBK1 PROTAC architecture;

FIG. 3. Snapshot of an aminopyrimidine TBK1 ligand bound to TBK1 (from41M0);

FIG. 4. Snapshot of hydroxyproline VHL ligand chemotype bound to VHL(from 4W9L);

FIG. 5. PROTAC 18 is a VHL incompetent epimer of active TBK1 degrader11;

FIG. 6. PROTAC 11 but not its VHL-incompetent epimer 18 nor TBK1inhibitor 1 effects degradation of TBK1. All 3 display competentintracellular TBK1/pIRF3 activity;

FIG. 7. PROTAC 11 mediated degradation of TBK1 is abrogated in thepresence of the proteasome inhibitor carfilzomib;

FIG. 8A TBK1 degradation in KRAS mutant and wild type cells; and FIG. 8BAntiproliferative effects of TBK1 degrader 11 on KRAS mutant and wildtype cells; and

FIG. 9. PROTAC 11 selectively degrades TBK1 over IKKε.

DETAILED DESCRIPTION

The following is a detailed description provided to aid those skilled inthe art in practicing the present invention. Those of ordinary skill inthe art may make modifications and variations in the embodimentsdescribed herein without departing from the spirit or scope of thepresent disclosure. All publications, patent applications, patents,figures and other references mentioned herein are expressly incorporatedby reference in their entirety.

The present description relates to the surprising and unexpecteddiscovery that an E3 ubiquitin ligase protein can ubiquitinate a targetprotein once the E3 ubiquitin ligase protein and the target protein arebrought into proximity by a chimeric construct (e.g., PROTAC) asdescribed herein, which binds the E3 ubiquitin ligase protein and thetarget protein. Accordingly, the present description provides compounds,compositions comprising the same, and associated methods of use forubiquitination and degradation of a chosen target protein, e.g., TBK1(See FIG. 1).

The present description is related in certain aspects to U.S. PatentPublication 2014/0356322A1, which is incorporated herein by reference inits entirety for all purposes.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. The terminology used in thedescription is for describing particular embodiments only and is notintended to be limiting of the invention.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise (such as in the case of a groupcontaining a number of carbon atoms in which case each carbon atomnumber falling within the range is provided), between the upper andlower limit of that range and any other stated or intervening value inthat stated range is encompassed within the invention. The upper andlower limits of these smaller ranges may independently be included inthe smaller ranges is also encompassed within the invention, subject toany specifically excluded limit in the stated range. Where the statedrange includes one or both of the limits, ranges excluding either bothof those included limits are also included in the invention.

The following terms are used to describe the present invention. Ininstances where a term is not specifically defined herein, that term isgiven an art-recognized meaning by those of ordinary skill applying thatterm in context to its use in describing the present invention.

The articles “a” and “an” as used herein and in the appended claims areused herein to refer to one or to more than one (i.e., to at least one)of the grammatical object of the article unless the context clearlyindicates otherwise. By way of example, “an element” means one elementor more than one element.

The phrase “and/or,” as used herein in the specification and in theclaims, should be understood to mean “either or both” of the elements soconjoined, i.e., elements that are conjunctively present in some casesand disjunctively present in other cases. Multiple elements listed with“and/or” should be construed in the same fashion, i.e., “one or more” ofthe elements so conjoined. Other elements may optionally be presentother than the elements specifically identified by the “and/or” clause,whether related or unrelated to those elements specifically identified.Thus, as a non-limiting example, a reference to “A and/or B”, when usedin conjunction with open-ended language such as “comprising” can refer,in one embodiment, to A only (optionally including elements other thanB); in another embodiment, to B only (optionally including elementsother than A); in yet another embodiment, to both A and B (optionallyincluding other elements); etc.

As used herein in the specification and in the claims, “or” should beunderstood to have the same meaning as “and/or” as defined above. Forexample, when separating items in a list, “or” or “and/or” shall beinterpreted as being inclusive, i.e., the inclusion of at least one, butalso including more than one, of a number or list of elements, and,optionally, additional unlisted items. Only terms clearly indicated tothe contrary, such as “only one of” or “exactly one of,” or, when usedin the claims, “consisting of,” will refer to the inclusion of exactlyone element of a number or list of elements. In general, the term “or”as used herein shall only be interpreted as indicating exclusivealternatives (i.e., “one or the other but not both”) when preceded byterms of exclusivity, such as “either,” “one of,” “only one of,” or“exactly one of.”

The term “about” and the like, as used herein, in association withnumeric values or ranges, reflects the fact that there is a certainlevel of variation that is recognized and tolerated in the art due topractical and/or theoretical limitations. For example, minor variationis tolerated due to inherent variances in the manner in which certaindevices operate and/or measurements are taken. In accordance with theabove, the phrase “about” is normally used to encompass values withinthe standard deviation or standard error.

In the claims, as well as in the specification above, all transitionalphrases such as “comprising,” “including,” “carrying,” “having,”“containing,” “involving,” “holding,” “composed of,” and the like are tobe understood to be open-ended, i.e., to mean including but not limitedto. Only the transitional phrases “consisting of” and “consistingessentially of” shall be closed or semi-closed transitional phrases,respectively, as set forth in the United States Patent Office Manual ofPatent Examining Procedures, Section 2111.03.

As used herein in the specification and in the claims, the phrase “atleast one,” in reference to a list of one or more elements, should beunderstood to mean at least one element selected from anyone or more ofthe elements in the list of elements, but not necessarily including atleast one of each and every element specifically listed within the listof elements and not excluding any combinations of elements in the listof elements. This definition also allows that elements may optionally bepresent other than the elements specifically identified within the listof elements to which the phrase “at least one” refers, whether relatedor unrelated to those elements specifically identified. Thus, as anonlimiting example, “at least one of A and B” (or, equivalently, “atleast one of A or B,” or, equivalently “at least one of A and/or B”) canrefer, in one embodiment, to at least one, optionally including morethan one, A, with no B present (and optionally including elements otherthan B); in another embodiment, to at least one, optionally includingmore than one, B, with no A present (and optionally including elementsother than A); in yet another embodiment, to at least one, optionallyincluding more than one, A, and at least one, optionally including morethan one, B (and optionally including other elements); etc.

It should also be understood that, in certain methods described hereinthat include more than one step or act, the order of the steps or actsof the method is not necessarily limited to the order in which the stepsor acts of the method are recited unless the context indicatesotherwise.

The terms “co-administration” and “co-administering” or “combinationtherapy” can refer to both concurrent administration (administration oftwo or more therapeutic agents at the same time) and time variedadministration (administration of one or more therapeutic agents at atime different from that of the administration of an additionaltherapeutic agent or agents), as long as the therapeutic agents arepresent in the patient to some extent, preferably at effective amounts,at the same time. In certain preferred aspects, one or more of thepresent compounds described herein, are co-administered in combinationwith at least one additional bioactive agent, especially including ananticancer agent. In particularly preferred aspects, theco-administration of compounds results in synergistic activity and/ortherapy, including anticancer activity.

The term “effective” can mean, but is in no way limited to, thatamount/dose of the active pharmaceutical ingredient, which, when used inthe context of its intended use, effectuates or is sufficient toprevent, inhibit the occurrence, ameliorate, delay or treat (alleviate asymptom to some extent, preferably all) the symptoms of a condition,disorder or disease state in a subject in need of such treatment orreceiving such treatment. The term effective subsumes all othereffective amount or effective concentration terms, e.g., “effectiveamount/dose,” “pharmaceutically effective amount/dose” or“therapeutically effective amount/dose,” which are otherwise describedor used in the present application.

The effective amount depends on the type and severity of disease, thecomposition used, the route of administration, the type of mammal beingtreated, the physical characteristics of the specific mammal underconsideration, concurrent medication, and other factors which thoseskilled in the medical arts will recognize. The exact amount can beascertainable by one skilled in the art using known techniques (see,e.g., Lieberman, Pharmaceutical Dosage Forms (vols. 1-3, 1992); Lloyd,The Art, Science and Technology of Pharmaceutical Compounding (1999);Pickar, Dosage Calculations (1999); and Remington: The Science andPractice of Pharmacy, 20th Edition, 2003, Gennaro, Ed., Lippincott,Williams & Wilkins).

The term “pharmacological composition,” “therapeutic composition,”“therapeutic formulation” or “pharmaceutically acceptable formulation”can mean, but is in no way limited to, a composition or formulation thatallows for the effective distribution of an agent provided by theinvention, which is in a form suitable for administration to thephysical location most suitable for their desired activity, e.g.,systemic administration.

The term “pharmaceutically acceptable” or “pharmacologically acceptable”can mean, but is in no way limited to, entities and compositions that donot produce an adverse, allergic or other untoward reaction whenadministered to an animal, or a human, as appropriate.

The term “pharmaceutically acceptable carrier” or “pharmacologicallyacceptable carrier” can mean, but is in no way limited to, any and allsolvents, dispersion media, coatings, antibacterial and antifungalagents, isotonic and absorption delaying agents, and the like,compatible with pharmaceutical administration. Suitable carriers aredescribed in the most recent edition of Remington's PharmaceuticalSciences, a standard reference text in the field, which is incorporatedherein by reference. Preferred examples of such carriers or diluentsinclude, but are not limited to, water, saline, finger's solutions,dextrose solution, and 5% human serum albumin. Liposomes and non-aqueousvehicles such as fixed oils may also be used. The use of such media andagents for pharmaceutically active substances is well known in the art.Except insofar as any conventional media or agent is incompatible withthe active compound, use thereof in the compositions is contemplated.Supplementary active compounds can also be incorporated into thecompositions.

The term “systemic administration” refers to a route of administrationthat is, e.g., enteral or parenteral, and results in the systemicdistribution of an agent leading to systemic absorption or accumulationof drugs in the blood stream followed by distribution throughout theentire body. Suitable forms, in part, depend upon the use or the routeof entry, for example oral, transdermal, or by injection. Such formsshould not prevent the composition or formulation from reaching a targetcell (i.e., a cell to which the negatively charged polymer is desired tobe delivered to). For example, pharmacological compositions injectedinto the blood stream should be soluble. Other factors are known in theart, and include considerations such as toxicity and forms which preventthe composition or formulation from exerting its effect. Administrationroutes which lead to systemic absorption include, without limitations:intravenous, subcutaneous, intraperitoneal, inhalation, oral,intrapulmonary and intramuscular. The rate of entry of a drug into thecirculation has been shown to be a function of molecular weight or size.The use of a liposome or other drug carrier comprising the compounds ofthe instant invention can potentially localize the drug, for example, incertain tissue types, such as the tissues of the reticular endothelialsystem (RES). A liposome formulation which can facilitate theassociation of drug with the surface of cells, such as, lymphocytes andmacrophages is also useful.

The term “local administration” refers to a route of administration inwhich the agent is delivered to a site that is apposite or proximal,e.g., within about 10 cm, to the site of the lesion or disease.

The term “compound”, as used herein, unless otherwise indicated, refersto any specific chemical compound disclosed herein and includestautomers, regioisomers, geometric isomers, and where applicable,stereoisomers, including optical isomers (enantiomers) and otherstereoisomers (diastereomers) thereof, as well as pharmaceuticallyacceptable salts and derivatives (including prodrug forms) thereof whereapplicable, in context. Within its use in context, the term compoundgenerally refers to a single compound, but also may include othercompounds such as stereoisomers, regioisomers and/or optical isomers(including racemic mixtures) as well as specific enantiomers orenantiomerically enriched mixtures of disclosed compounds. The term alsorefers, in context to prodrug forms of compounds which have beenmodified to facilitate the administration and delivery of compounds to asite of activity. It is noted that in describing the present compounds,numerous substituents and variables associated with same, among others,are described.

It is understood by those of ordinary skill that molecules which aredescribed herein are stable compounds as generally described hereunder.When the bond

is shown, both a double bond and single bond are represented within thecontext of the compound shown.

As used herein, “derivatives” can mean compositions formed from thenative compounds either directly, by modification, or by partialsubstitution. As used herein, “analogs” can mean compositions that havea structure similar to, but not identical to, the native compound.

The term “Ubiquitin Ligase” refers to a family of proteins thatfacilitate the transfer of ubiquitin to a specific substrate protein,targeting the substrate protein for degradation. For example, VonHippel-Lindau E3 Ubiquitin Ligase or VCB E3 Ubiquitin Ligase is proteinthat alone or in combination with an E2 ubiquitin-conjugating enzymecauses the attachment of ubiquitin to a lysine on a target protein, andsubsequently targets the specific protein substrates for degradation bythe proteasome. Thus, E3 ubiquitin ligase alone or in complex with an E2ubiquitin conjugating enzyme is responsible for the transfer ofubiquitin to targeted proteins. In general, the ubiquitin ligase isinvolved in polyubiquitination such that a second ubiquitin is attachedto the first; a third is attached to the second, and so forth.Polyubiquitination marks proteins for degradation by the proteasome.However, there are some ubiquitination events that are limited tomono-ubiquitination, in which only a single ubiquitin is added by theubiquitin ligase to a substrate molecule. Mono-ubiquitinated proteinsare not targeted to the proteasome for degradation, but may instead bealtered in their cellular location or function, for example, via bindingother proteins that have domains capable of binding ubiquitin. Furthercomplicating matters, different lysines on ubiquitin can be targeted byan E3 to make chains. The most common lysine is Lys48 on the ubiquitinchain. This is the lysine used to make polyubiquitin, which isrecognized by the proteasome.

The term “subject” is used throughout the specification to describe acell, tissue, or animal, preferably a human or a domesticated animal, towhom treatment, including prophylactic treatment, with the compositionsaccording to the present invention is provided. For treatment of thoseinfections, conditions or disease states which are specific for aspecific animal such as a human patient, the term patient refers to thatspecific animal, including a domesticated animal such as a dog or cat ora farm animal such as a horse, cow, sheep, etc. In general, in thepresent invention, the term patient refers to a human patient unlessotherwise stated or implied from the context of the use of the term.

Compounds

In one aspect, the present invention provides compounds useful forregulating protein activity. The composition comprises a ubiquitinpathway protein binding moiety (preferably for an E3 ubiquitin ligase,alone or in complex with an E2 ubiquitin conjugating enzyme which isresponsible for the transfer of ubiquitin to targeted proteins)according to a defined chemical structure and a protein targeting moietywhich are linked or coupled together, preferably through a linker,wherein the ubiquitin pathway protein binding moiety recognizes anubiquitin pathway protein and the targeting moiety recognizes a targetprotein (e.g., TBK1).

In certain embodiments, the disclosure provides compounds which functionto recruit TBK1 proteins to E3 Ubiquitin Ligase for ubiquintination anddegradation. In certain embodiments, the compounds have the followinggeneral structure:

TBM-L-ULM  (I),

wherein ULM is an E3 ligase binding moiety, e.g., a moiety that binds amember selected from the group of Von Hippel-Lindau (VHL) E3 ubiquitinligase, cereblon, IAP (XIAP), and MDM2, TBM is a TBK1 binding moiety,which binds to a TBK1 protein and L is a bond or a chemical linkermoiety which links the TBM and ULM.

Without being bound by any particular theory, it is hypothesized thatdue at least in part to the proximity of TBK1 and the E3 ubiquitinligase, the TBK1 is ubiquitinated by the ubiquitin ligase and degraded.In certain embodiments, the TBM is chemically linked or coupled directlyto the ULM group. In certain additional embodiments, the TBM ischemically linked or coupled to the ULM via a chemical linker moiety.

The von Hippel-Lindau (VHL) tumor suppressor. VHL comprises thesubstrate recognition subunit/E3 ligase complex VCB, which includeselongins B and C, and a complex including Cullin-2 and Rbx1. The primarysubstrate of VHL is Hypoxia Inducible Factor 1α (HIF-1α), atranscription factor that upregulates genes such as the pro-angiogenicgrowth factor VEGF and the red blood cell inducing cytokineerythropoietin in response to low oxygen levels. We generated the firstsmall molecule ligands of Von Hippel Lindau (VHL) to the substraterecognition subunit of the E3 ligase, VCB, an important target incancer, chronic anemia and ischemia, and obtained crystal structuresconfirming that the compound mimics the binding mode of thetranscription factor HIF-1α, the major substrate of VHL.

Inhibitors of Apoptosis Protein (IAPs) are guardian ubiquitin ligasesthat keep classic pro-apoptotic proteins in check, and regulates notonly caspases and apoptosis, but also modulates inflammatory signalingand immunity, copper homeostasis, mitogenic kinase signaling, cellproliferation, as well as cell invasion and metastasis. IAPs act as adirect caspase inhibitor, and directly bind to the active site pocket ofCASP3 and CASP7 and obstruct substrate entry. IAPS also inactivate CASP9by keeping it in a monomeric, inactive state. IAP acts as an E3ubiquitin-protein ligase regulating NF-kappa-B signaling and the targetproteins for its E3 ubiquitin-protein ligase activity include: RIPK1,CASP3, CASP7, CASP8, CASP9, MAP3K2/MEKK2, DIABLO/SMAC, AIFM1, CCS andBIRC5/survivin. Ubiquitination of CCS leads to enhancement of itschaperone activity toward its physiologic target, SOD1, rather thanproteasomal degradation. Ubiquitinion of MAP3K2/MEKK2 and AIFM1 does notlead to proteasomal degradation. IAP plays a role in copper homeostasisby ubiquitinating COMMD1 and promoting its proteasomal degradation, andcan also function as E3 ubiquitin-protein ligase of the NEDD8conjugation pathway, targeting effector caspases for neddylation andinactivation. IAP regulates the BMP signaling pathway and the SMAD andMAP3K7/TAK1 dependent pathways leading to NF-kappa-B and JNK activation.

IAPs are an important regulator of innate immune signaling viaregulation of Nodlike receptors (NLRs), and protects cells fromspontaneous formation of the ripoptosome, a large multi-protein complexthat has the capability to kill cancer cells in a caspase-dependent andcaspase-independent manner. Suppresses ripoptosome formation byubiquitinating RIPK1 and CASP8. Acts as a positive regulator of Wntsignaling and ubiquitinates TLE1, TLE2, TLE3, TLE4 and AES.Ubiquitination of TLE3 results in inhibition of its interaction withTCF7L2/TCF4 thereby allowing efficient recruitment and binding of thetranscriptional coactivator beta-catenin to TCF7L2/TCF4 that is requiredto initiate a Wnt-specific transcriptional program. Inhibitors of theIAP, which are useful in making compounds as described herein, are knownin the art.

Mouse double minute 2 homolog (MDM2) also known as E3 ubiquitin-proteinligase Mdm2 is a protein that in humans is encoded by the MDM2 gene.Mdm2 is an important negative regulator of the p53 tumor suppressor.Mdm2 protein functions both as an E3 ubiquitin ligase that recognizesthe N-terminal trans-activation domain (TAD) of the p53 tumor suppressorand an inhibitor of p53 transcriptional activation. Inhibitors of theMDM2-p53 interaction, which are useful in making compounds as describedherein, include the cis-imidazoline analog nutlin.

Cereblon is a protein that in humans is encoded by the CRBN gene. CRBNorthologs are highly conserved from plants to humans, which underscoresits physiological importance. Cereblon forms an E3 ubiquitin ligasecomplex with damaged DNA binding protein 1 (DDB1), Cullin-4A (CUL4A),and regulator of cullins 1 (ROC1). This complex ubiquitinates a numberof other proteins. Through a mechanism which has not been completelyelucidated, cereblon ubquitination of target proteins results inincreased levels of fibroblast growth factor 8 (FGF8) and fibroblastgrowth factor 10 (FGF10). FGF8 in turn regulates a number ofdevelopmental processes, such as limb and auditory vesicle formation.The net result is that this ubiquitin ligase complex is important forlimb outgrowth in embryos. In the absence of cereblon, DDB1 forms acomplex with DDB2 that functions as a DNA damage-binding protein.

Thalidomide, which has been approved for the treatment of a number ofimmunological indications, has also been approved for the treatment ofcertain neoplastic diseases, including multiple myeloma. In addition tomultiple myeloma, thalidomide and several of its analogs are alsocurrently under investigation for use in treating a variety of othertypes of cancer. While the precise mechanism of thalidomide's anti-tumoractivity is still emerging, it is known to inhibit angiogenesis. Recentliterature discussing the biology of the imides includes Lu et alScience 343, 305 (2014) and Kronke et al Science 343, 301 (2014).

Significantly, thalidomide and its analogs e.g. pomolinamiode andlenalinomide, are known to bind cereblon. These agents bind to cereblon,altering the specificity of the complex to induce the ubiquitination anddegradation of Ikaros (IKZF1) and Aiolos (IKZF3), transcription factorsessential for multiple myeloma growth. Indeed, higher expression ofcereblon has been linked to an increase in efficacy of imide drugs inthe treatment of multiple myeloma. Therefore, thalidomide and itsanalogs are useful cereblon binding moieties for use in making compoundsas described herein.

In additional embodiments, the description provides compounds having thefollowing general structure:

TBM-L-VLM  (II),

wherein TBM is a TBK1 binding moiety and VLM is a Von Hippel-Lindau E3Ubiquitin Ligase binding moiety, and L is a bond or a chemical linkermoiety which links the TBM and VLM. The ULM or VLM group and TBM groupmay be covalently linked to the linker group through any covalent bondwhich is appropriate and stable to the chemistry of the linker.

In certain embodiments, the bifunctional compound further comprises achemical linker (“L”). In this example, the structure of thebifunctional compound can be depicted as:

TBM-L-CLM  (II),

wherein TBM is a TBK1 binding moiety, L is a linker, and CLM is acereblon E3 ubiquitin ligase binding moiety.

It will be understood that the general structures are exemplary and therespective moieties can be arranged in any desired order orconfiguration, e.g., ULM-L-TBM, and VLM-L-TBM respectively. In certainadditional embodiments, the compounds comprise a plurality of E3 ligasebinding moieties and/or a plurality of TBMs.

In any of the aspects or embodiments of compounds described herein,unless indicated otherwise, the compounds are intended to encompasspharmaceutically acceptable salts, enantiomers, stereoisomers, solvatesor polymorphs thereof.

Exemplary ULMs

In certain embodiments of the compounds as described herein, the ULMcomprises a chemical structure selected from the group ULM-a:

wherein:

-   -   a dashed line indicates the attachment of at least one TBM,        another ULM or VLM (i.e., ULM′ or VLM′), or a chemical linker        moiety coupling at least one TBM, a ULM′ or VLM′ to the other        end of the linker;    -   X¹, X² are each independently a bond, O, NR^(Y3), CR^(Y3)R^(Y4),        C═O, C═S, SO, SO₂;    -   R^(Y3), R^(Y4) are each independently H, C₁₋₆ alkyl (linear,        branched, optionally substituted by 1 or more halo, C₁₋₆        alkoxyl);    -   optionally substituted by 1-3 R^(P) groups in the pyrrolidine        moiety, wherein each R^(P) is independently H, halo, —OH,        C₁₋₃alkyl;    -   W³ is an optionally substituted -T-N(R^(1a)R^(1b)), -T-Aryl, an        optionally substituted -T-Heteroaryl, an optionally substituted        -T-Heterocycle, an optionally substituted —NR¹-T-Aryl, an        optionally substituted —NR¹-T-Heteroaryl or an optionally        substituted —NR¹-T-Heterocycle, where T is covalently bonded to        X¹;    -   each R¹, R^(1a), R^(1b) is independently H, a C1-C6 alkyl group        (linear, branched, optionally substituted by 1 or more halo,        —OH), R^(Y3)C═O, R^(Y3)C═S, R^(Y3)SO, R^(Y3)SO₂,        N(R^(Y3)R^(Y4))C═O, N(R^(Y3)R^(Y4))C═S, N(R^(Y3)R^(Y4))SO,        N(R^(Y3)R^(Y4))SO₂;    -   T is an optionally substituted —(CH₂)_(n)— group, wherein each        one of the methylene groups may be optionally substituted with        one or two substituents, preferably selected from halogen, a        C1-C6 alkyl group (linear, branched, optionally substituted by 1        or more halogen, —OH) or the sidechain of an amino acid as        otherwise described herein, preferably methyl, which may be        optionally substituted; and n is 0 to 6, often 0, 1, 2, or 3,        preferably 0.

Alternatively, T may also be a —(CH₂O)_(n)— group, a —(OCH₂)_(n)— group,a —(CH₂CH₂O)_(n)-group, a —(OCH₂CH₂)_(n)— group, each of which groups isoptionally substituted; and

W⁴ is an optionally substituted —NR¹-T-Aryl, an optionally substituted—NR¹-T-Heteroaryl group or an optionally substituted —NR¹-T-Heterocycle,where where —NR¹ is covalently bonded to X²; R¹ is H or CH₃, preferablyH, and T is an optionally substituted —(CH₂)_(n)— group, wherein eachone of the methylene groups may be optionally substituted with one ortwo substituents, preferably selected from halogen, an amino acidsidechain as otherwise described herein or a C1-C6 alkyl group (linear,branched, optionally substituted by 1 or more halo, —OH), preferably oneor two methyl groups, which may be optionally substituted; and n is 0 to6, often 0, 1, 2 or 3, preferably 0 or 1.

Alternatively, T may also be a —(CH₂O)_(n)— group, a —(OCH₂)_(n)— group,a —(CH₂CH₂O)_(n)— group, a —(OCH₂CH₂)_(n)— group, all of which groupsare optionally substituted.

In any of the embodiments described herein, W³ and/or W⁴ can be attachedto a linker moiety as described herein.

In certain embodiments, aryl groups for W³ include optionallysubstituted phenyl or naphthyl groups, preferably phenyl groups, whereinthe phenyl or naphthyl group is optionally substituted with a linkergroup to which is attached a TBM group (including a ULM′ group) and/or ahalogen (preferably F or Cl), an amine, monoalkyl- or dialkyl amine(preferably, dimethylamine), an amido group (preferably a—(CH₂)_(m)—NR₁C(O)R₂ group where m, R₁ and R₂ are the same as for R¹), ahalogen (often F or Cl), OH, CH₃, CF₃, OMe, OCF₃, NO₂, CN or aS(O)₂R_(S) group (R_(S) is a a C₁-C₆ alkyl group, an optionallysubstituted aryl, heteroaryl or heterocycle group or a —(CH₂)_(m)NR₁R₂group), each of which may be substituted in ortho-, meta- and/orpara-positions of the phenyl ring, preferably para-), or an Aryl(preferably phenyl), heteroaryl or heterocycle. Preferably saidsubstituent phenyl group is an optionally substituted phenyl group(i.e., the substituent phenyl group itself is preferably substitutedwith at least one of F, Cl, OH, SH, COOH, CH₃, CF₃, OMe, OCF₃, NO₂, CNor a linker group to which is attached a TBM group (including a ULM′group), wherein the substitution occurs in ortho-, meta- and/orpara-positions of the phenyl ring, preferably para-, a naphthyl group,which may be optionally substituted including as described above, anoptionally substituted heteroaryl (preferably an optionally substitutedisoxazole including a methylsubstituted isoxazole, an optionallysubstituted oxazole including a methylsubstituted oxazole, an optionallysubstituted thiazole including a methyl substituted thiazole, anoptionally substituted pyrrole including a methylsubstituted pyrrole, anoptionally substituted imidazole including a methylimidazole, abenzylimidazole or methoxybenzylimidazole, an oximidazole ormethyloximidazole, an optionally substituted diazole group, including amethyldiazole group, an optionally substituted triazole group, includinga methylsubstituted triazole group, a pyridine group, including a halo-(preferably, F) or methylsubstitutedpyridine group or an oxapyridinegroup (where the pyridine group is linked to the phenyl group by anoxygen) or an optionally substituted heterocycle (tetrahydrofuran,tetrahydrothiophene, pyrrolidine, piperidine, morpholine, piperazine,tetrahydroquinoline, oxane or thiane. Each of the aryl, heteroaryl orheterocyclic groups may be optionally substituted with a linker group towhich is attached a TBM group (including a ULM′ group).

In certain embodiments, heteroaryl groups for W³ include an optionallysubstituted quinoline (which may be attached to the pharmacophore orsubstituted on any carbon atom within the quinoline ring), an optionallysubstituted indole (including dihydroindole), an optionally substitutedindolizine, an optionally substituted azaindolizine (2, 3 or4-azaindolizine) an optionally substituted benzimidazole, benzodiazole,benzoxofuran, an optionally substituted imidazole, an optionallysubstituted isoxazole, an optionally substituted oxazole (preferablymethyl substituted), an optionally substituted diazole, an optionallysubstituted triazole, a tetrazole, an optionally substituted benzofuran,an optionally substituted thiophene, an optionally substituted thiazole(preferably methyl and/or thiol substituted), an optionally substitutedisothiazole, an optionally substituted triazole (preferably a1,2,3-triazole substituted with a methyl group, a triisopropylsilylgroup, an optionally substituted —(CH₂)_(m)O—C₁-C₆ alkyl group or anoptionally substituted —(CH₂)_(m)C(O)—O—C₁-C₆ alkyl group), anoptionally substituted pyridine (2-, 3, or 4-pyridine) or a groupaccording to the chemical structure:

wherein:

-   -   S^(c) is CHR^(SS), NR^(URE), or O;    -   R^(HET) is H, CN, NO₂, halo (preferably Cl or F), optionally        substituted C₁-C₆ alkyl (preferably substituted with one or two        hydroxyl groups or up to three halo groups (e.g. CF₃),        optionally substituted O(C₁-C₆ alkyl) (preferably substituted        with one or two hydroxyl groups or up to three halo groups) or        an optionally substituted acetylenic group —C≡C—R_(a) where        R_(a) is H or a C₁-C₆ alkyl group (preferably C₁-C₃ alkyl);    -   R^(SS) is H, CN, NO₂, halo (preferably F or Cl), optionally        substituted C₁-C₆ alkyl (preferably substituted with one or two        hydroxyl groups or up to three halo groups), optionally        substituted O—(C₁-C₆ alkyl) (preferably substituted with one or        two hydroxyl groups or up to three halo groups) or an optionally        substituted —C(O)(C₁-C₆ alkyl) (preferably substituted with one        or two hydroxyl groups or up to three halo groups);    -   R^(URE) is H, a C₁-C₆ alkyl (preferably H or C₁-C₃ alkyl) or a        —C(O)(C₁-C₆ alkyl), each of which groups is optionally        substituted with one or two hydroxyl groups or up to three        halogen, preferably fluorine groups, or an optionally        substituted heterocycle, for example piperidine, morpholine,        pyrrolidine, tetrahydrofuran, tetrahydrothiophene, piperidine,        piperazine, each of which is optionally substituted; and    -   Y^(C) is N or C—R^(YC), where R^(YC) is H, OH, CN, NO₂, halo        (preferably Cl or F), optionally substituted C₁-C₆ alkyl        (preferably substituted with one or two hydroxyl groups or up to        three halo groups (e.g. CF₃), optionally substituted O(C₁-C₆        alkyl) (preferably substituted with one or two hydroxyl groups        or up to three halo groups) or an optionally substituted        acetylenic group —C≡C—R_(a) where R_(a) is H or a C₁-C₆ alkyl        group (preferably C₁-C₃ alkyl). Each of said heteroaryl groups        may be optionally substituted with a linker group to which is        attached a TBM group (including a ULM′ group).

In additional embodiments, heterocycle groups for W³ includetetrahydroquinoline, piperidine, piperazine, pyrrollidine, morpholine,tetrahydrofuran, tetrahydrothiophene, oxane and thiane, each of whichgroups may be optionally substituted or a group according to thechemical structure:

wherein:

-   -   R^(PRO) is H, optionally substituted C₁-C₆ alkyl or an        optionally substituted aryl (phenyl or napthyl), heteroaryl or        heterocyclic group selected from the group consisting of        oxazole, isoxazole, thiazole, isothiazole, imidazole, diazole,        oximidazole, pyrrole, pyrollidine, furan, dihydrofuran,        tetrahydrofuran, thiene, dihydrothiene, tetrahydrothiene,        pyridine, piperidine, piperazine, morpholine, quinoline, (each        preferably substituted with a C₁-C₃ alkyl group, preferably        methyl or a halo group, preferably F or Cl), benzofuran, indole,        indolizine, azaindolizine;    -   R^(PRO1) and R^(PRO2) are each independently H, an optionally        substituted C₁-C₃ alkyl group or together form a keto group, and        each n is 0, 1, 2, 3, 4, 5, or 6 (preferably 0 or 1), wherein        each of said Heterocycle groups may be optionally substituted        with a linker group to which is attached a TBM group (including        a ULM′ group) or a pharmaceutically acceptable salt,        stereoisomer, solvate or polymorph thereof.

In certain embodiments, W³ substituents for use in the present inventionalso include specifically (and without limitation to the specificcompound disclosed) the W³ substituents which are found in theidentified compounds disclosed herein (which includes the specificcompounds which are disclosed in the present specification, and thefigures which are attached hereto). Each of these W³ substituents may beused in conjunction with any number of W⁴ substituents, which are alsodisclosed herein.

In certain embodiments, Aryl groups for W⁴ include optionallysubstituted phenyl or naphthyl groups, preferably phenyl groups, whereinthe phenyl group is optionally substituted with a linker group to whichis attached an TBMTBM group (including a ULM′ group), a halogen(preferably F or Cl), an amine, monoalkyl- or dialkyl amine (preferably,dimethylamine), F, Cl, OH, COOH, C₁-C₆ alkyl, preferably CH₃, CF₃, OMe,OCF₃, NO₂, or CN group (each of which may be substituted in ortho-,meta- and/or para-positions of the phenyl ring, preferably para-), anoptionally substituted phenyl group (the phenyl group itself ispreferably substituted with a linker group attached to a TBM group,including a ULM′ group), and/or at least one of F, Cl, OH, COOH, CH₃,CF₃, OMe, OCF₃, NO₂, or CN group (in ortho-, meta- and/or para-positionsof the phenyl ring, preferably para-), a naphthyl group, which may beoptionally substituted, an optionally substituted heteroaryl, preferablyan optionally substituted isoxazole including a methylsubstitutedisoxazole, an optionally substituted oxazole including amethylsubstituted oxazole, an optionally substituted thiazole includinga methyl substituted thiazole, an optionally substituted isothiazoleincluding a methyl substituted isothiazole, an optionally substitutedpyrrole including a methylsubstituted pyrrole, an optionally substitutedimidazole including a methylimidazole, an optionally substitutedbenzimidazole or methoxybenzylimidazole, an optionally substitutedoximidazole or methyloximidazole, an optionally substituted diazolegroup, including a methyldiazole group, an optionally substitutedtriazole group, including a methylsubstituted triazole group, anoptionally substituted pyridine group, including a halo-(preferably, F)or methylsubstitutedpyridine group or an oxapyridine group (where thepyridine group is linked to the phenyl group by an oxygen), anoptionally substituted furan, an optionally substituted benzofuran, anoptionally substituted dihydrobenzofuran, an optionally substitutedindole, indolizine or azaindolizine (2, 3, or 4-azaindolizine), anoptionally substituted quinoline, an optionally substituted groupaccording to the chemical structure:

wherein:

-   -   S^(c) is CHR^(SS), NR^(URE), or O;    -   R^(HET) is H, CN, NO₂, halo (preferably Cl or F), optionally        substituted C₁-C₆ alkyl (preferably substituted with one or two        hydroxyl groups or up to three halo groups (e.g. CF₃),        optionally substituted O(C₁-C₆ alkyl) (preferably substituted        with one or two hydroxyl groups or up to three halo groups) or        an optionally substituted acetylenic group —C≡C—R_(a) where        R_(a) is H or a C₁-C₆ alkyl group (preferably C₁-C₃ alkyl);    -   R^(SS) is H, CN, NO₂, halo (preferably F or Cl), optionally        substituted C₁-C₆ alkyl (preferably substituted with one or two        hydroxyl groups or up to three halo groups), optionally        substituted O—(C₁-C₆ alkyl) (preferably substituted with one or        two hydroxyl groups or up to three halo groups) or an optionally        substituted —C(O)(C₁-C₆ alkyl) (preferably substituted with one        or two hydroxyl groups or up to three halo groups);    -   R^(URE) is H, a C₁-C₆ alkyl (preferably H or C₁-C₃ alkyl) or a        —C(O)(C₁-C₆ alkyl) each of which groups is optionally        substituted with one or two hydroxyl groups or up to three        halogen, preferably fluorine groups, or an optionally        substituted phenyl group, an optionally substituted heteroaryl,        or an optionally substituted heterocycle, preferably for example        piperidine, morpholine, pyrrolidine, tetrahydrofuran);    -   ^(PRO) is H, optionally substituted C₁-C₆ alkyl or an optionally        substituted aryl (phenyl or napthyl), heteroaryl or heterocyclic        group selected from the group consisting of oxazole, isoxazole,        thiazole, isothiazole, imidazole, diazole, oximidazole, pyrrole,        pyrollidine, furan, dihydrofuran, tetrahydrofuran, thiene,        dihydrothiene, tetrahydrothiene, pyridine, piperidine,        piperazine, morpholine, quinoline, (each preferably substituted        with a C₁-C₃ alkyl group, preferably methyl or a halo group,        preferably F or Cl), benzofuran, indole, indolizine,        azaindolizine;    -   R^(PRO)1 and R^(PRO2) are each independently H, an optionally        substituted C₁-C₃ alkyl group or together form a keto group; and    -   each n is independently 0, 1, 2, 3, 4, 5, or 6 (preferably 0 or        1), or an optionally substituted heterocycle, preferably        tetrahydrofuran, tetrahydrothiene, piperidine, piperazine or        morpholine (each of which groups when substituted, are        preferably substituted with a methyl or halo (F, Br, Cl), each        of which groups may be optionally substituted with a linker        group to which is attached a TBM group (including a ULM′ group).

In certain preferred aspects,

where R^(PRO) and n are the same as above.

In certain embodiments, heteroaryl groups for W⁴ include an optionallysubstituted quinoline (which may be attached to the pharmacophore orsubstituted on any carbon atom within the quinoline ring), an optionallysubstituted indole, an optionally substituted indolizine, an optionallysubstituted azaindolizine, an optionally substituted benzofuran,including an optionally substituted benzofuran, an optionallysubstituted isoxazole, an optionally substituted thiazole, an optionallysubstituted isothiazole, an optionally substituted thiophene, anoptionally substituted pyridine (2-, 3, or 4-pyridine), an optionallysubstituted imidazole, an optionally substituted pyrrole, an optionallysubstituted diazole, an optionally substituted triazole, a tetrazole, anoptionally substituted oximidazole, or a group according to the chemicalstructure:

wherein:

-   -   S^(c) is CHR^(SS), NR^(URE), or O;    -   ^(HET) is H, CN, NO₂, halo (preferably Cl or F), optionally        substituted C₁-C₆ alkyl (preferably substituted with one or two        hydroxyl groups or up to three halo groups (e.g. CF₃),        optionally substituted O(C₁-C₆ alkyl) (preferably substituted        with one or two hydroxyl groups or up to three halo groups) or        an optionally substituted acetylenic group —C≡C—R_(a) where        R_(a) is H or a C₁-C₆ alkyl group (preferably C₁-C₃ alkyl);    -   R^(SS) is H, CN, NO₂, halo (preferably F or Cl), optionally        substituted C₁-C₆ alkyl (preferably substituted with one or two        hydroxyl groups or up to three halo groups), optionally        substituted O—(C₁-C₆ alkyl) (preferably substituted with one or        two hydroxyl groups or up to three halo groups) or an optionally        substituted —C(O)(C₁-C₆ alkyl) (preferably substituted with one        or two hydroxyl groups or up to three halo groups);    -   R^(URE) is H, a C₁-C₆ alkyl (preferably H or C₁-C₃ alkyl) or a        —C(O)(C₁-C₆ alkyl), each of which groups is optionally        substituted with one or two hydroxyl groups or up to three        halogen, preferably fluorine groups, or an optionally        substituted heterocycle, for example piperidine, morpholine,        pyrrolidine, tetrahydrofuran, tetrahydrothiophene, piperidine,        piperazine, each of which is optionally substituted, and    -   Y^(C) is N or C—R^(YC), where R^(YC) is H, OH, CN, NO₂, halo        (preferably Cl or F), optionally substituted C₁-C₆ alkyl        (preferably substituted with one or two hydroxyl groups or up to        three halo groups (e.g. CF₃), optionally substituted O(C₁-C₆        alkyl) (preferably substituted with one or two hydroxyl groups        or up to three halo groups) or an optionally substituted        acetylenic group —C≡C—R_(a) where R_(a) is H or a C₁-C₆ alkyl        group (preferably C₁-C₃ alkyl), each of which groups may be        optionally substituted with a linker group to which is attached        a TBM group (including a ULM′ group).

In certain embodiments, heterocycle groups for W⁴ includetetrahydrofuran, tetrahydrothiene, tetrahydroquinoline, piperidine,piperazine, pyrrollidine, morpholine, oxane or thiane, each of whichgroups may be optionally substituted, or a group according to thechemical structure:

preferably, a

wherein:

-   -   R^(PRO) is H, optionally substituted C₁-C₆ alkyl or an        optionally substituted aryl, heteroaryl or heterocyclic group;    -   R^(PRO1) and R^(PRO2) are each independently H, an optionally        substituted C₁-C₃ alkyl group or together form a keto group and    -   each n is independently 0, 1, 2, 3, 4, 5, or 6 (often 0 or 1),        each of which groups may be optionally substituted with a linker        group to which is attached a TBM group (including a ULM′ group)        In additional embodiments, W⁴ substituents for use in the        present invention also include specifically (and without        limitation to the specific compound disclosed) the W⁴        substituents which are found in the identified compounds        disclosed herein (which includes the specific compounds which        are disclosed in the present specification, and the figures        which are attached hereto). Each of these W⁴ substituents may be        used in conjunction with any number of W³ substituents which are        also disclosed herein.

In certain additional embodiments, ULM-a, is optionally substituted by1-3 R^(P) groups in the pyrrolidine moiety. Each R^(P) is independentlyH, halo, —OH, C₁₋₃alkyl.

In any of the embodiments described herein, the W³, W⁴ can independentlybe covalently coupled to a linker which is attached one or more TBMgroups.

In certain embodiments, ULM is a group (derivatized or configured to belinked or coupled to an TBM via a linker (as indicated by the dashedline) according to the chemical structure:

wherein:

-   -   W³ is optionally substituted aryl, optionally substituted        heteroaryl, or

-   -   each R₉ and R₁₀ is independently hydrogen, optionally        substituted alkyl, optionally substituted cycloalkyl, optionally        substituted hydroxyalkyl, optionally substituted heteroaryl, or        haloalkyl; or R₉, R₁₀, and the carbon atom to which they are        attached form an optionally substituted cycloalkyl;    -   R₁₁ is optionally substituted heterocyclic, optionally        substituted alkoxy, optionally substituted heteroaryl,        optionally substituted aryl,

-   -   R₁₂ is H or optionally substituted alkyl;    -   R₁₃ is H, optionally substituted alkyl, optionally substituted        alkylcarbonyl, optionally substituted (cycloalkyl)alkylcarbonyl,        optionally substituted aralkylcarbonyl, optionally substituted        arylcarbonyl, optionally substituted (heterocyclyl)carbonyl, or        optionally substituted aralkyl;    -   R_(14a), R_(14b), is each independently H, haloalkyl, or        optionally substituted alkyl;    -   W⁵ is a phenyl or a 5-10 membered heteroaryl,    -   R₁₅ is H, halogen, CN, OH, NO₂, N R_(14a)R_(14b), OR_(14a),        CONR_(14a)R_(14b), NR_(14a)COR_(14b), SO₂NR_(14a)R_(14b),        NR_(14a)SO₂R_(14b), optionally substituted alkyl, optionally        substituted haloalkyl, optionally substituted haloalkoxy; aryl,        heteroaryl, cycloalkyl, cycloheteroalkyl;    -   each R₁₆ is independently halo, optionally substituted alkyl,        optionally substituted haloalkyl, hydroxy, or optionally        substituted haloalkoxy;    -   o is 0, 1, 2, 3, or 4;    -   each R₁₈ is independently halo, optionally substituted alkoxy,        cyano, optionally substituted alkyl, haloalkyl, haloalkoxy or a        linker; and    -   p is 0, 1, 2, 3, or 4.

In certain embodiments, R₁₅ is

wherein R₁₇ is H, halo, optionally substituted C₃₋₆cycloalkyl,optionally substituted C₁₋₆alkyl, optionally substituted C₁₋₆alkenyl,and C₁₋₆haloalkyl; and Xa is S or 0.

In certain embodiments, R₁₇ is selected from the group methyl, ethyl,isopropyl, and cyclopropyl.

In certain additional embodiments, R₁₅ is selected from the groupconsisting of:

In certain embodiments, R₁₁ is selected from the group consisting of:

In certain embodiments, the ULM (derivatized or configured to be linkedor coupled to an TBM via a linker (as indicated by the dashed line)) hasthe structure:

wherein:

-   -   R_(14a) is independently H, haloalkyl, methyl, or optionally        substituted alkyl;    -   R₁₅ is

wherein R₁₇ is H, halo, optionally substituted C₃₋₆cycloalkyl,optionally substituted C₁₋₆alkyl, optionally substituted C₁₋₆alkenyl,and C₁₋₆haloalky

-   -   R₁₇ is methyl, ethyl, isopropyl, or cyclopropyl;    -   R₉ is H;    -   R₁₀ is isopropyl, tert-butyl, sec-butyl, cyclopentyl, or        cyclohexyl;    -   R₁₁ is

-   -   R₁₂ is H    -   R₁₃ is H, optionally substituted alkyl, optionally substituted        alkylcarbonyl, optionally substituted (cycloalkyl)alkylcarbonyl,        optionally substituted aralkylcarbonyl, optionally substituted        arylcarbonyl, optionally substituted (heterocyclyl)carbonyl, or        optionally substituted aralkyl; and

In certain embodiments, the ULM or VLM is selected from the groupconsisting of:

attached to the linker moiety at the position indicated.

In one aspect the description provides compounds useful for bindingand/or inhibiting cereblon. In certain embodiments, the compound isselected from the group consisting of chemical structures:

wherein:

-   -   W is independently selected from the group CH₂, CHR, C═O, SO₂,        NH, and N-alkyl;    -   X is independently selected from the group, S and H₂;    -   Y is independently selected from the group NH, N-alkyl, N-aryl,        N-hetaryl, N-cycloalkyl, N-heterocyclyl, O, and S;    -   Z is independently selected from the group, and S or H₂ except        that both X and Z cannot be H₂;    -   G and G′ are independently selected from the group H, alkyl, OH,        CH₂-heterocyclyl optionally substituted with R′, and benzyl        optionally substituted with R′; Q1-Q4 represent a carbon C        substituted with a group independently selected from R′, N or        N-oxide;    -   A is independently selected from the group alkyl, cycloalkyl, Cl        and F;    -   R comprises, but is not limited to: —CONR′R″, —OR′, —NR′R″,        —SR′, —SO₂R′, —SO₂NR′R″, —CR′R″—, —CR′NR′R″—, -aryl, -hetaryl,        -alkyl, -cycloalkyl, -heterocyclyl, —P(O)(OR′)R″, —P(O)R′R″,        —OP(O)(OR′)R″, —OP(O)R′R″, —Cl, —F, —Br, —I, —CF₃, —CN,        —NR′SO₂NR′R″, —NR′CONR′R″, —CONR′COR″, —NR′C(═N—CN)NR′R″,        —C(═N—CN)NR′R″, —NR′C(═N—CN)R″, —NR′C(═C—NO₂)NR′R″, —SO₂NR′COR″,        —NO₂, —CO₂R′, —C(C═N—OR′)R″, —CR′═CR′R″, —CCR′,        —S(C═O)(C═N—R′)R″, —SF₅ and —OCF₃    -   R′ and R″ are independently selected from a bond, H, alkyl,        cycloalkyl, aryl, hetaryl, heterocyclyl    -   n is an integer from 1-4;    -   represents a bond that may be stereospecific ((R) or (S)) or        non-stereospecific; and    -   R_(n) comprises 1-4 independent functional groups or atoms.

In any of the compounds described herein, the CLM comprises a chemicalstructure selected from the group:

wherein:

-   -   W is independently selected from the group CH₂, CHR, C═O, SO₂,        NH, and N-alkyl;    -   X is independently selected from the group O, S and H2;    -   Y is independently selected from the group NH, N-alkyl, N-aryl,        N-hetaryl, N-cycloalkyl, N-heterocyclyl, O, and S;    -   Z is independently selected from the group O, and S or H2 except        that both X and Z cannot be H2;    -   G and G′ are independently selected from the group H, alkyl, OH,        CH₂-heterocyclyl optionally substituted with R′, and benzyl        optionally substituted with R′;    -   Q1-Q4 represent a carbon C substituted with a group        independently selected from R′, N or N-oxide;    -   A is independently selected from the group alkyl, cycloalkyl, Cl        and F;    -   R comprises, but is not limited to: —CONR′R″, —OR′, —NR′R″,        —SR′, —SO₂R′, —SO₂NR′R″, —CR′R″—, —CR′NR′R″—, -aryl, -hetaryl,        -alkyl, -cycloalkyl, -heterocyclyl, —P(O)(OR′)R″, —P(O)R′R″,        —OP(O)(OR′)R″, —OP(O)R′R″, —Cl, —F, —Br, —I, —CF3, —CN,        —NR′SO₂NR′R″, —NR′CONR′R″, —CONR′COR″, —NR′C(═N—CN)NR′R″,        —C(═N—CN)NR′R″, —NR′C(═N—CN)R″, —NR′C(═C—NO₂)NR′R″, —SO₂NR′COR″,        —NO₂, —CO2R′, —C(C═N—OR′)R″, —CR′═CR′R″, —CCR′,        —S(C═O)(C═N—R′)R″, —SF5 and —OCF3    -   R′ and R″ are independently selected from a bond, H, alkyl,        cycloalkyl, aryl, hetaryl, heterocyclyl    -   n is an integer from 1-4;    -   represents a bond that may be stereospecific ((R) or (S)) or        non-stereospecific; and    -   Rn comprises 1-4 independent functional groups or atoms, and        optionally, one of which is modified to be covalently joined to        a PTM, a chemical linker group (L), a ULM, CLM (or CLM′) or        combination thereof.

Exemplary Linkers

In certain embodiments, the compounds as described herein include one ormore TBM chemically linked or coupled to one or more ULMs or VLMs via achemical linker (L). In certain embodiments, the linker group L is agroup comprises one or more covalently connected structural units of A(e.g. -A_(1 . . .) A_(q)-), wherein A₁ is coupled to an TBM moiety, andq is an integer greater than or equal to 0. In certain embodiments, q isan integer greater than or equal to 1.

In certain embodiments, e. g., where q is greater than 2, A_(q) is agroup which is connected to a ULM or VLM moiety, and A₁ and A_(q) areconnected via structural units of A (number of such structural units ofA: q−2).

In certain embodiments, e. g., where q is 2, A_(q) is a group which isconnected to A₁ and to a ULM or VLM moiety.

In certain embodiments, e. g., where q is 1, the structure of the linkergroup L is -A₁-, and A₁ is a group which is connected to a ULM or VLMmoiety and an TBM moiety.

In additional embodiments, q is an integer from 1 to 100, 1 to 90, 1 to80, 1 to 70, 1 to 60, 1 to 50, 1 to 40, 1 to 30, 1 to 20, or 1 to 10.

In certain embodiments, A₁ to A_(q) are, each independently, a bond,CR^(L1)R^(L2), O, S, SO, SO₂, NR^(L3), SO₂NR^(L3), SONR^(L3), CONR^(L3),NR^(L3)CONR^(L4), NR^(L3)SO₂NR^(L4), CO, CR^(L1)═CR^(L2), C≡C,SiR^(L1)R^(L2), P(O)R^(L1), P(O)OR^(L1), NR^(L3)C(═NCN)NR^(L4),NR^(L3)C(═NCN), NR^(L3)C(═CNO₂)NR^(L4), C₃₋₁₁cycloalkyl optionallysubstituted with 0-6 R^(L1) and/or R^(L2) groups, C₃₋₁₁heteocyclyloptionally substituted with 0-6 R^(L1) and/or R^(L2) groups, aryloptionally substituted with 0-6 R^(L1) and/or R^(L2) groups, heteroaryloptionally substituted with 0-6 R^(L1) and/or R^(L2) groups, whereinR^(L1) or R^(L) ₂, each independently, can be linked to other A groupsto form cycloalkyl and/or heterocyclyl moeity which can be furthersubstituted with 0-4 R^(L1) groups;

wherein R^(L1), R^(L2), R^(L3), R^(L4) and R^(L5) are, eachindependently, H, halo, C₁₋₈alkyl, OC₁₋₈alkyl, SC₁₋₈alkyl, NHC₁₋₈alkyl,N(C₁₋₈alkyl)₂, C₃₋₁₁cycloalkyl, aryl, heteroaryl, C₃₋₁₁heterocyclyl,OC₁₋₈cycloalkyl, SC₁₋₈cycloalkyl, NHC₁₋₈cycloalkyl, N(C₁₋₈cycloalkyl)₂,N(C₁₋₈cycloalkyl)(C₁₋₈alkyl), OH, NH₂, SH, SO₂C₁₋₈alkyl,P(O)(OC₁₋₈alkyl)(C₁₋₈alkyl), P(O)(OC₁₋₈alkyl)₂, CC—C₁₋₈alkyl, CCH,CH═CH(C₁₋₈alkyl), C(C₁₋₈alkyl)═CH(C₁₋₈alkyl),C(C₁₋₈alkyl)═C(C₁₋₈alkyl)₂, Si(OH)₃, Si(C₁₋₈alkyl)₃, Si(OH)(C₁₋₈alkyl)₂,COC₁₋₈alkyl, CO₂H, halogen, CN, CF₃, CHF₂, CH₂F, NO₂, SF₅,SO₂NHC₁₋₈alkyl, SO₂N(C₁₋₈alkyl)₂, SON(C₁₋₈alkyl, SON(C₁₋₈alkyl)₂,CONHC₁₋₈alkyl, CON(C₁₋₈alkyl)₂, N(C₁₋₈alkyl)CONH(C₁₋₈alkyl),N(C₁₋₈alkyl)CON(C₁₋₈alkyl)₂, NHCONH(C₁₋₈alkyl), NHCON(C₁₋₈alkyl)₂,NHCONH₂, N(C₁₋₈alkyl)SO₂NH(C₁₋₈alkyl), N(C₁₋₈alkyl) SO₂N(C₁₋₈alkyl)₂, NHSO₂NH(C₁₋₈alkyl), NH SO₂N(C₁₋₈alkyl)₂, NH SO₂NH₂.

In certain embodiments, the linker (L) is selected from the groupconsisting of):

In additional embodiments, the linker group is optionally substituted(poly)ethyleneglycol having between 1 and about 100 ethylene glycolunits, between about 1 and about 50 ethylene glycol units, between 1 andabout 25 ethylene glycol units, between about 1 and 10 ethylene glycolunits, between 1 and about 8 ethylene glycol units and 1 and 6 ethyleneglycol units, between 2 and 4 ethylene glycol units, or optionallysubstituted alkyl groups interdispersed with optionally substituted, O,N, S, P or Si atoms. In certain embodiments, the linker is substitutedwith an aryl, phenyl, benzyl, alkyl, alkylene, or heterocycle group. Incertain embodiments, the linker may be asymmetric or symmetrical.

In another embodiment, the present invention provides a library ofcompounds. The library comprises more than one compound wherein eachcompound has a formula of TBM-L-ULM, wherein ULM is a ubiquitin pathwayprotein binding moiety (preferably, an E3 ubiquitin ligase moiety asotherwise disclosed herein), e.g., a VLM, and TBM is an TBK1 proteinbinding moiety, wherein TBM is coupled (preferably, through a linkermoiety) to ULM, and wherein the ubiquitin pathway protein binding moietyrecognizes an ubiquitin pathway protein, in particular, an E3 ubiquitinligase.

The present description includes, where applicable, the compositionscomprising the pharmaceutically acceptable salts, in particular, acid orbase addition salts of compounds of the present invention.

The term “pharmaceutically acceptable salt” is used throughout thespecification to describe, where applicable, a salt form of one or moreof the compounds described herein which are presented to increase thesolubility of the compound in the gastic juices of the patient'sgastrointestinal tract in order to promote dissolution and thebioavailability of the compounds. Pharmaceutically acceptable saltsinclude those derived from pharmaceutically acceptable inorganic ororganic bases and acids, where applicable. Suitable salts include thosederived from alkali metals such as potassium and sodium, alkaline earthmetals such as calcium, magnesium and ammonium salts, among numerousother acids and bases well known in the pharmaceutical art. Sodium andpotassium salts are particularly preferred as neutralization salts ofthe phosphates according to the present invention.

The acids which are used to prepare the pharmaceutically acceptable acidaddition salts of the aforementioned base compounds useful in thisinvention are those which form non-toxic acid addition salts, i.e.,salts containing pharmacologically acceptable anions, such as thehydrochloride, hydrobromide, hydroiodide, nitrate, sulfate, bisulfate,phosphate, acid phosphate, acetate, lactate, citrate, acid citrate,tartrate, bitartrate, succinate, maleate, fumarate, gluconate,saccharate, benzoate, methanesulfonate, ethanesulfonate,benzenesulfonate, p-toluenesulfonate and pamoate [i.e.,1,1′-methylene-bis-(2-hydroxy-3 naphthoate)]salts, among numerousothers.

Pharmaceutically acceptable base addition salts may also be used toproduce pharmaceutically acceptable salt forms of the compounds orderivatives according to the present invention. The chemical bases thatmay be used as reagents to prepare pharmaceutically acceptable basesalts of the present compounds that are acidic in nature are those thatform non-toxic base salts with such compounds. Such non-toxic base saltsinclude, but are not limited to those derived from suchpharmacologically acceptable cations such as alkali metal cations (eg.,potassium and sodium) and alkaline earth metal cations (eg, calcium,zinc and magnesium), ammonium or water-soluble amine addition salts suchas N-methylglucamine-(meglumine), and the lower alkanolammonium andother base salts of pharmaceutically acceptable organic amines, amongothers.

Compositions

In another aspect, the description provides compositions comprisingcompounds as described herein, including salts thereof, and apharmaceutically acceptable carrier. In certain embodiments, thecompositions are therapeutic or pharmaceutical compositions comprisingan effective amount of a compound as described herein and apharmaceutally acceptable carrier.

The amount of compound in a pharmaceutical composition of the instantinvention that may be combined with the carrier materials to produce asingle dosage form will vary depending upon the host and diseasetreated, the particular mode of administration. Generally, an amountbetween 0.1 mg/kg and 1000 mg/kg body weight/day of active ingredientsis administered dependent upon potency of the agent. Toxicity andtherapeutic efficacy of such compounds can be determined by standardpharmaceutical procedures in cell cultures or experimental animals,e.g., for determining the LD50 (the dose lethal to 50% of thepopulation) and the ED50 (the dose therapeutically effective in 50% ofthe population). The dose ratio between toxic and therapeutic effects isthe therapeutic index and it can be expressed as the ratio LD50/ED50.Compounds that exhibit large therapeutic indices are preferred. Whilecompounds that exhibit toxic side effects may be used, care should betaken to design a delivery system that targets such compounds to thesite of affected tissue in order to minimize potential damage touninfected cells and, thereby, reduce side effects. The data obtainedfrom the cell culture assays and animal studies can be used informulating a range of dosage for use in humans. The dosage of suchcompounds lies preferably within a range of circulating concentrationsthat include the ED50 with little or no toxicity. The dosage may varywithin this range depending upon the dosage form employed and the routeof administration utilized. For any compound used in the method of theinvention, the therapeutically effective dose can be estimated initiallyfrom cell culture assays. A dose may be formulated in animal models toachieve a circulating plasma concentration range that includes the IC50(i.e., the concentration of the test compound which achieves ahalf-maximal inhibition of symptoms) as determined in cell culture. Suchinformation can be used to more accurately determine useful doses inhumans. Levels in plasma may be measured, for example, by highperformance liquid chromatography.

The compositions of the present invention may be formulated in aconventional manner using one or more pharmaceutically acceptablecarriers and may also be administered in controlled-releaseformulations. Pharmaceutically acceptable carriers that may be used inthese pharmaceutical compositions include, but are not limited to, ionexchangers, alumina, aluminum stearate, lecithin, serum proteins, suchas human serum albumin, buffer substances such as phosphates, glycine,sorbic acid, potassium sorbate, partial glyceride mixtures of saturatedvegetable fatty acids, water, salts or electrolytes, such as prolaminesulfate, disodium hydrogen phosphate, potassium hydrogen phosphate,sodium chloride, zinc salts, colloidal silica, magnesium trisilicate,polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol,sodium carboxymethylcellulose, polyacrylates, waxes,polyethylene-polyoxypropylene-block polymers, polyethylene glycol andwool fat.

The active compound is included in the pharmaceutically acceptablecarrier or diluent in an amount sufficient to deliver to a patient atherapeutically effective amount for the desired indication, withoutcausing serious toxic effects in the patient treated. A preferred doseof the active compound for all of the herein-mentioned conditions is inthe range from about 10 ng/kg to 300 mg/kg, preferably 0.1 to 100 mg/kgper day, more generally 0.5 to about 25 mg per kilogram body weight ofthe recipient/patient per day. A typical topical dosage will range from0.01-5% wt/wt in a suitable carrier.

The compound is conveniently administered in any suitable unit dosageform, including but not limited to one containing less than 1 mg, 1 mgto 3000 mg, preferably 5 to 500 mg of active ingredient per unit dosageform. An oral dosage of about 25-250 mg is often convenient.

The active ingredient is preferably administered to achieve peak plasmaconcentrations of the active compound of about 0.00001-30 mM, preferablyabout 0.1-30 μM. This may be achieved, for example, by the intravenousinjection of a solution or formulation of the active ingredient,optionally in saline, or an aqueous medium or administered as a bolus ofthe active ingredient. Oral administration is also appropriate togenerate effective plasma concentrations of active agent.

The concentration of active compound in the drug composition will dependon absorption, distribution, inactivation, and excretion rates of thedrug as well as other factors known to those of skill in the art. It isto be noted that dosage values will also vary with the severity of thecondition to be alleviated. It is to be further understood that for anyparticular subject, specific dosage regimens should be adjusted overtime according to the individual need and the professional judgment ofthe person administering or supervising the administration of thecompositions, and that the concentration ranges set forth herein areexemplary only and are not intended to limit the scope or practice ofthe claimed composition. The active ingredient may be administered atonce, or may be divided into a number of smaller doses to beadministered at varying intervals of time.

If administered intravenously, preferred carriers are physiologicalsaline or phosphate buffered saline (PBS).

In one embodiment, the active compounds are prepared with carriers thatwill protect the compound against rapid elimination from the body, suchas a controlled release formulation, including implants andmicroencapsulated delivery systems. Biodegradable, biocompatiblepolymers can be used, such as ethylene vinyl acetate, polyanhydrides,polyglycolic acid, collagen, polyorthoesters, and polylactic acid.Methods for preparation of such formulations will be apparent to thoseskilled in the art.

Liposomal suspensions may also be pharmaceutically acceptable carriers.These may be prepared according to methods known to those skilled in theart, for example, as described in U.S. Pat. No. 4,522,811 (which isincorporated herein by reference in its entirety). For example, liposomeformulations may be prepared by dissolving appropriate lipid(s) (such asstearoyl phosphatidyl ethanolamine, stearoyl phosphatidyl choline,arachadoyl phosphatidyl choline, and cholesterol) in an inorganicsolvent that is then evaporated, leaving behind a thin film of driedlipid on the surface of the container. An aqueous solution of the activecompound are then introduced into the container. The container is thenswirled by hand to free lipid material from the sides of the containerand to disperse lipid aggregates, thereby forming the liposomalsuspension.

Modes of Administration

In any of the aspects or embodiments described herein, the therapeuticcompositions comprising compounds described herein can be in anysuitable dosage form configured to be delivered by any suitable route.For example, the compounds can be administered by any appropriate route,for example, orally, parenterally, intravenously, intradermally,subcutaneously, or topically, including transdermally, in liquid, cream,gel, or solid form, rectally, nasally, buccally, vaginally or via animplanted reservoir or by aerosol form.

The term “parenteral” as used herein includes subcutaneous, intravenous,intramuscular, intra-articular, intra-synovial, intrasternal,intrathecal, intrahepatic, intralesional and intracranial injection orinfusion techniques. Preferably, the compositions are administeredorally, intraperitoneally or intravenously.

The compounds as described herein may be administered in single ordivided doses by the oral, parenteral or topical routes. Administrationof the active compound may range from continuous (intravenous drip) toseveral oral administrations per day (for example, Q.I.D.) and mayinclude oral, topical, parenteral, intramuscular, intravenous,sub-cutaneous, transdermal (which may include a penetration enhancementagent), buccal, sublingual and suppository administration, among otherroutes of administration. Enteric coated oral tablets may also be usedto enhance bioavailability of the compounds from an oral route ofadministration. The most effective dosage form will depend upon thepharmacokinetics of the particular agent chosen as well as the severityof disease in the patient.

Administration of compounds as sprays, mists, or aerosols forintra-nasal, intra-tracheal or pulmonary administration may also beused. Compounds as described herein may be administered in immediaterelease, intermediate release or sustained or controlled release forms.Sustained or controlled release forms are preferably administeredorally, but also in suppository and transdermal or other topical forms.Intramuscular injections in liposomal form may also be used to controlor sustain the release of compound at an injection site.

Sterile injectable forms of the compositions as described herein may beaqueous or oleaginous suspension. These suspensions may be formulatedaccording to techniques known in the art using suitable dispersing orwetting agents and suspending agents. The sterile injectable preparationmay also be a sterile injectable solution or suspension in a non-toxicparenterally-acceptable diluent or solvent, for example as a solution in1, 3-butanediol. Among the acceptable vehicles and solvents that may beemployed are water, Ringer's solution and isotonic sodium chloridesolution. In addition, sterile, fixed oils are conventionally employedas a solvent or suspending medium. For this purpose, any bland fixed oilmay be employed including synthetic mono- or di-glycerides. Fatty acids,such as oleic acid and its glyceride derivatives are useful in thepreparation of injectables, as are natural pharmaceutically-acceptableoils, such as olive oil or castor oil, especially in theirpolyoxyethylated versions. These oil solutions or suspensions may alsocontain a long-chain alcohol diluent or dispersant, such as Ph. Helv orsimilar alcohol.

The pharmaceutical compositions as described herein may be orallyadministered in any orally acceptable dosage form including, but notlimited to, capsules, tablets, aqueous suspensions or solutions. In thecase of tablets for oral use, carriers which are commonly used includelactose and corn starch. Lubricating agents, such as magnesium stearate,are also typically added. For oral administration in a capsule form,useful diluents include lactose and dried corn starch. When aqueoussuspensions are required for oral use, the active ingredient is combinedwith emulsifying and suspending agents. If desired, certain sweetening,flavoring or coloring agents may also be added. Oral compositions willgenerally include an inert diluent or an edible carrier. They may beenclosed in gelatin capsules or compressed into tablets. For the purposeof oral therapeutic administration, the active compound or its prodrugderivative can be incorporated with excipients and used in the form oftablets, troches, or capsules. Pharmaceutically compatible bindingagents, and/or adjuvant materials are included as part of thecomposition.

The tablets, pills, capsules, troches and the like can contain any ofthe following ingredients, or compounds of a similar nature: a bindersuch as microcrystalline cellulose, gum tragacanth or gelatin; anexcipient such as starch or lactose, a dispersing agent such as alginicacid, Primogel, or corn starch; a lubricant such as magnesium stearateor Sterotes; a glidant such as colloidal silicon dioxide; a sweeteningagent such as sucrose or saccharin; or a flavoring agent such aspeppermint, methyl salicylate, or orange flavoring. When the dosage unitform is a capsule, it can contain, in addition to material of the abovetype, a liquid carrier such as a fatty oil. In addition, dosage unitforms can contain various other materials which modify the physical formof the dosage unit, for example, coatings of sugar, shellac, or entericagents.

The active compound or pharmaceutically acceptable salt thereof can beadministered as a component of an elixir, suspension, syrup, wafer,chewing gum or the like. A syrup may contain, in addition to the activecompounds, sucrose as a sweetening agent and certain preservatives, dyesand colorings and flavors.

Alternatively, the pharmaceutical compositions as described herein maybe administered in the form of suppositories for rectal administration.These can be prepared by mixing the agent with a suitable non-irritatingexcipient, which is solid at room temperature but liquid at rectaltemperature and therefore will melt in the rectum to release the drug.Such materials include cocoa butter, beeswax and polyethylene glycols.

The pharmaceutical compositions of this invention may also beadministered topically. Suitable topical formulations are readilyprepared for each of these areas or organs. Topical application for thelower intestinal tract can be effected in a rectal suppositoryformulation (see above) or in a suitable enema formulation.Topically-acceptable transdermal patches may also be used. For topicalapplications, the pharmaceutical compositions may be formulated in asuitable ointment containing the active component suspended or dissolvedin one or more carriers. Carriers for topical administration of thecompounds of this invention include, but are not limited to, mineraloil, liquid petrolatum, white petrolatum, propylene glycol,polyoxyethylene, polyoxypropylene compound, emulsifying wax and water.In certain preferred aspects of the invention, the compounds may becoated onto a stent which is to be surgically implanted into a patientin order to inhibit or reduce the likelihood of occlusion occurring inthe stent in the patient.

Alternatively, the pharmaceutical compositions can be formulated in asuitable lotion or cream containing the active components suspended ordissolved in one or more pharmaceutically acceptable carriers. Suitablecarriers include, but are not limited to, mineral oil, sorbitanmonostearate, polysorbate 60, cetyl esters wax, cetearyl alcohol,2-octyldodecanol, benzyl alcohol and water.

For ophthalmic use, the pharmaceutical compositions may be formulated asmicronized suspensions in isotonic, pH adjusted sterile saline, or,preferably, as solutions in isotonic, pH adjusted sterile saline, eitherwith our without a preservative such as benzylalkonium chloride.Alternatively, for ophthalmic uses, the pharmaceutical compositions maybe formulated in an ointment such as petrolatum.

The pharmaceutical compositions of this invention may also beadministered by nasal aerosol or inhalation. Such compositions areprepared according to techniques well-known in the art of pharmaceuticalformulation and may be prepared as solutions in saline, employing benzylalcohol or other suitable preservatives, absorption promoters to enhancebioavailability, fluorocarbons, and/or other conventional solubilizingor dispersing agents.

Solutions or suspensions used for parenteral, intradermal, subcutaneous,or topical application can include the following components: a sterilediluent such as water for injection, saline solution, fixed oils,polyethylene glycols, glycerine, propylene glycol or other syntheticsolvents; antibacterial agents such as benzyl alcohol or methylparabens; antioxidants such as ascorbic acid or sodium bisulfite;chelating agents such as ethylenediaminetetraacetic acid; buffers suchas acetates, citrates or phosphates and agents for the adjustment oftonicity such as sodium chloride or dextrose. The parental preparationcan be enclosed in ampoules, disposable syringes or multiple dose vialsmade of glass or plastic.

It should also be understood that a specific dosage and treatmentregimen for any particular patient will depend upon a variety offactors, including the activity of the specific compound employed, theage, body weight, general health, sex, diet, time of administration,rate of excretion, drug combination, and the judgment of the treatingphysician and the severity of the particular disease or condition beingtreated.

A patient or subject in need of therapy using compounds as describedherein can be treated by administering to the patient (subject) aneffective amount of the compound including pharmaceutically acceptablesalts, solvates or polymorphs, thereof optionally in a pharmaceuticallyacceptable carrier or diluent, either alone, or in combination withother known agents.

Co-Administration

Disease states of conditions which may be treated using compounds orcompositions according to the present description include, but notlimited to, for example, cancer (e.g., prostate cancer), and Kennedy'sdisease. In certain embodiments, the therapeutic or pharmaceuticalcompositions comprise an effective amount of an additional biologicallyor bioactive active agent, e.g., an agent effective for the treatment ofcancer, that is co-administered.

The term “coadministration” or “combination therapy” shall mean that atleast two compounds or compositions are administered to the patient atthe same time, such that effective amounts or concentrations of each ofthe two or more compounds may be found in the patient at a given pointin time. Although compounds according to the present invention may beco-administered to a patient at the same time, the term embraces bothadministration of two or more agents at the same time or at differenttimes, provided that effective concentrations of all coadministeredcompounds or compositions are found in the subject at a given time. Incertain preferred aspects of the present invention, one or more of thepresent compounds described above, are coadministered in combinationwith at least one additional bioactive agent, especially including ananticancer agent. In particularly preferred aspects of the invention,the co-administration of compounds results in synergistic therapeutic,including anticancer therapy.

In another aspect, the description provides a composition comprising aneffective amount of two or more of the PROTAC compounds as describedherein, and a pharmaceutically acceptable carrier. In certainembodiments, the composition further comprises an effective orsynergistic amount of another bioactive agent that is not a PROTACcompound.

Pharmaceutical compositions comprising combinations of an effectiveamount of at least one bifunctional compound according to the presentinvention, and one or more of the compounds otherwise described herein,all in effective amounts, in combination with a pharmaceuticallyeffective amount of a carrier, additive or excipient, represents afurther aspect of the present invention.

The term “bioactive agent” is used to describe an agent, other than thePROTAC compounds described herein, which is used in combination with thepresent compounds as an agent with biological activity to assist ineffecting an intended therapy, inhibition and/or prevention/prophylaxisfor which the present compounds are used. Preferred bioactive agents foruse herein include those agents which have pharmacological activitysimilar to that for which the present compounds are used or administeredand include for example, anti-cancer agents.

The term “additional anti-cancer agent” is used to describe ananti-cancer agent, which may be combined with PROTAC compounds accordingto the present description to treat cancer. These agents include, forexample, everolimus, trabectedin, abraxane, TLK 286, AV-299, DN-101,pazopanib, GSK690693, RTA 744, ON 0910.Na, AZD 6244 (ARRY-142886),AMN-107, TKI-258, GSK461364, AZD 1152, enzastaurin, vandetanib, ARQ-197,MK-0457, MLN8054, PHA-739358, R-763, AT-9263, a FLT-3 inhibitor, anandrogen receptor inhibitor, a VEGFR inhibitor, an EGFR TK inhibitor, anaurora kinase inhibitor, a PIK-1 modulator, a Bcl-2 inhibitor, an HDACinhbitor, a c-MET inhibitor, a PARP inhibitor, a Cdk inhibitor, an EGFRTK inhibitor, an IGFR-TK inhibitor, an anti-HGF antibody, a PI3 kinaseinhibitors, an AKT inhibitor, a JAK/STAT inhibitor, a checkpoint-1 or 2inhibitor, a focal adhesion kinase inhibitor, a Map kinase kinase (mek)inhibitor, a VEGF trap antibody, pemetrexed, erlotinib, dasatanib,nilotinib, decatanib, panitumumab, amrubicin, oregovomab, Lep-etu,nolatrexed, azd2171, batabulin, ofatumumab, zanolimumab, edotecarin,tetrandrine, rubitecan, tesmilifene, oblimersen, ticilimumab,ipilimumab, gossypol, Bio 111, 131-I-TM-601, ALT-110, BIO 140, CC 8490,cilengitide, gimatecan, IL13-PE38QQR, INO 1001, IPdR₁ KRX-0402,lucanthone, LY317615, neuradiab, vitespan, Rta 744, Sdx 102, talampanel,atrasentan, Xr 311, romidepsin, ADS-100380, sunitinib, 5-fluorouracil,vorinostat, etoposide, gemcitabine, doxorubicin, liposomal doxorubicin,5′-deoxy-5-fluorouridine, vincristine, temozolomide, ZK-304709,seliciclib; PD0325901, AZD-6244, capecitabine, L-Glutamic acid,N-[4-[2-(2-amino-4,7-dihydro-4-oxo-1H—pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl]-, disodium salt,heptahydrate, camptothecin, PEG-labeled irinotecan, tamoxifen,toremifene citrate, anastrazole, exemestane, letrozole,DES(diethylstilbestrol), estradiol, estrogen, conjugated estrogen,bevacizumab, IMC-1C11, CHIR-258);3-[5-(methylsulfonylpiperadinemethyl)-indolylj-quinolone, vatalanib,AG-013736, AVE-0005, the acetate salt of [D-Ser(But) 6, Azgly 10](pyro-Glu-His-Trp-Ser-Tyr-D-Ser(But)-Leu-Arg-Pro-Azgly-NH 2 acetate[C₉H₈₄N₁₈Oi₄-(C₂H₄O₂)_(x) where x=1 to 2.4], goserelin acetate,leuprolide acetate, triptorelin pamoate, medroxyprogesterone acetate,hydroxyprogesterone caproate, megestrol acetate, raloxifene,bicalutamide, flutamide, nilutamide, megestrol acetate, CP-724714;TAK-165, HKI-272, erlotinib, lapatanib, canertinib, ABX-EGF antibody,erbitux, EKB-569, PKI-166, GW-572016, Ionafarnib, BMS-214662,tipifarnib; amifostine, NVP-LAQ824, suberoyl analide hydroxamic acid,valproic acid, trichostatin A, FK-228, SU11248, sorafenib, KRN951,aminoglutethimide, arnsacrine, anagrelide, L-asparaginase, BacillusCalmette-Guerin (BCG) vaccine, adriamycin, bleomycin, buserelin,busulfan, carboplatin, carmustine, chlorambucil, cisplatin, cladribine,clodronate, cyproterone, cytarabine, dacarbazine, dactinomycin,daunorubicin, diethylstilbestrol, epirubicin, fludarabine,fludrocortisone, fluoxymesterone, flutamide, gleevec, gemcitabine,hydroxyurea, idarubicin, ifosfamide, imatinib, leuprolide, levamisole,lomustine, mechlorethamine, melphalan, 6-mercaptopurine, mesna,methotrexate, mitomycin, mitotane, mitoxantrone, nilutamide, octreotide,oxaliplatin, pamidronate, pentostatin, plicamycin, porfimer,procarbazine, raltitrexed, rituximab, streptozocin, teniposide,testosterone, thalidomide, thioguanine, thiotepa, tretinoin, vindesine,13-cis-retinoic acid, phenylalanine mustard, uracil mustard,estramustine, altretamine, floxuridine, 5-deooxyuridine, cytosinearabinoside, 6-mecaptopurine, deoxycoformycin, calcitriol, valrubicin,mithramycin, vinblastine, vinorelbine, topotecan, razoxin, marimastat,COL-3, neovastat, BMS-275291 squalamine, endostatin, SU5416, SU6668,EMD121974, interleukin-12, IM862, angiostatin, vitaxin, droloxifene,idoxyfene, spironolactone, finasteride, cimitidine, trastuzumab,denileukin diftitox,gefitinib, bortezimib, paclitaxel, cremophor-freepaclitaxel, docetaxel, epithilone B, BMS-247550, BMS-310705,droloxifene, 4-hydroxytamoxifen, pipendoxifene, ERA-923, arzoxifene,fulvestrant, acolbifene, lasofoxifene, idoxifene, TSE-424, HMR-3339,ZK186619, topotecan, PTK787/ZK 222584, VX-745, PD 184352, rapamycin,40-O-(2-hydroxyethyl)-rapamycin, temsirolimus, AP-23573, RAD001,ABT-578, BC-210, LY294002, LY292223, LY292696, LY293684, LY293646,wortmannin, ZM336372, L-779,450, PEG-filgrastim, darbepoetin,erythropoietin, granulocyte colony-stimulating factor, zolendronate,prednisone, cetuximab, granulocyte macrophage colony-stimulating factor,histrelin, pegylated interferon alfa-2a, interferon alfa-2a, pegylatedinterferon alfa-2b, interferon alfa-2b, azacitidine, PEG-L-asparaginase,lenalidomide, gemtuzumab, hydrocortisone, interleukin-11, dexrazoxane,alemtuzumab, all-transretinoic acid, ketoconazole, interleukin-2,megestrol, immune globulin, nitrogen mustard, methylprednisolone,ibritgumomab tiuxetan, androgens, decitabine, hexamethylmelamine,bexarotene, tositumomab, arsenic trioxide, cortisone, editronate,mitotane, cyclosporine, liposomal daunorubicin, Edwina-asparaginase,strontium 89, casopitant, netupitant, an NK-1 receptor antagonist,palonosetron, aprepitant, diphenhydramine, hydroxyzine, metoclopramide,lorazepam, alprazolam, haloperidol, droperidol, dronabinol,dexamethasone, methylprednisolone, prochlorperazine, granisetron,ondansetron, dolasetron, tropisetron, pegfilgrastim, erythropoietin,epoetin alfa, darbepoetin alfa and mixtures thereof.

Methods of Treatment

In another aspect, the disclosure provides methods of modulating proteinubiquitination and degradation in a subject, e.g., a cell, a tissue,mammal, or human patient, the method comprising administering aneffective amount of a compound as described herein or a compositioncomprising an effective amount of the same to a subject, wherein thecompound or composition comprising the same is effective in modulatingprotein ubquitination and degration of the protein in the subject. Incertain embodiments, the protein is TBK1.

In certain embodiments, the description provides a method for regulatingprotein activity of TBK1 in a patient in need comprising administeringto said patient an amount of a compound as described herein to apatient.

In still additional embodiments, the description provides a method oftreating a disease state or condition in a patient wherein dysregulatedprotein activity is responsible for said disease state or condition,said method comprising administering to said patient an effective amountof a compound as described herein to said patient in order to regulatesaid protein activity in said patient. In certain embodiments, theprotein is TBK1.

The terms “treat”, “treating”, and “treatment”, etc., as used herein,refer to any action providing a benefit to a patient for which thepresent compounds may be administered, including the treatment of anydisease state or condition which is modulated through the protein towhich the present compounds bind. Disease states or conditions,including cancer, which may be treated using compounds according to thepresent invention are set forth hereinabove.

In another aspect, the disclosure provides methods of modulating ARprotein ubiquitination and degradation in a subject, e.g., a cell, atissue, mammal, or human patient, the method comprising administering aneffective amount of a compound as described herein or a compositioncomprising an effective amount of the same to a subject, wherein thecompound or composition comprising the same is effective in modulatingAR protein ubquitination and degration of the protein in the subject.

In another aspect, the disclosure provides methods of treating orameliorating a symptom of a disease related to TBK1 activity in asubject, e.g., a cell, a tissue, mammal, or human patient, the methodcomprising administering an effective amount of a compound as describedherein or a composition comprising an effective amount of the same to asubject in need thereof, wherein the compound or composition comprisingthe same is effective in treating or ameliorating a symptom of a diseaserelated to TBK1 activity in the subject.

In certain embodiments, the disease or disorder is asthma, multiplesclerosis, cancer, prostate cancer, Kenney's disease, ciliopathies,cleft palate, diabetes, heart disease, hypertension, inflammatory boweldisease, mental retardation, mood disorder, obesity, refractive error,infertility, Angelman syndrome, Canavan disease, Coeliac disease,Charcot-Marie-Tooth disease, Cystic fibrosis, Duchenne musculardystrophy, Haemochromatosis, Haemophilia, Klinefelter's syndrome,Neurofibromatosis, Phenylketonuria, Polycystic kidney disease, (PKD1) or4 (PKD2) Prader-Willi syndrome, Sickle-cell disease, Tay-Sachs disease,Turner syndrome. In an embodiment, said cancer is squamous-cellcarcinoma, basal cell carcinoma, adenocarcinoma, hepatocellularcarcinomas, and renal cell carcinomas, cancer of the bladder, bowel,breast, cervix, colon, esophagus, head, kidney, liver, lung, neck,ovary, pancreas, prostate, and stomach; leukemias; benign and malignantlymphomas, particularly Burkitt's lymphoma and Non-Hodgkin's lymphoma;benign and malignant melanomas; myeloproliferative diseases; sarcomas,including Ewing's sarcoma, hemangiosarcoma, Kaposi's sarcoma,liposarcoma, myosarcomas, peripheral neuroepithelioma, synovial sarcoma,gliomas, astrocytomas, oligodendrogliomas, ependymomas, gliobastomas,neuroblastomas, ganglioneuromas, gangliogliomas, medulloblastomas,pineal cell tumors, meningiomas, meningeal sarcomas, neurofibromas, andSchwannomas; bowel cancer, breast cancer, prostate cancer, cervicalcancer, uterine cancer, lung cancer, ovarian cancer, testicular cancer,thyroid cancer, astrocytoma, esophageal cancer, pancreatic cancer,stomach cancer, liver cancer, colon cancer, melanoma; carcinosarcoma,Hodgkin's disease, Wilms' tumor or teratocarcinomas. In certainembodiments, the disease to be treated is cancer, e.g., prostate cancer,or Kennedy's Disease. In a preferred embodiment, the subject is a human.

In another aspect, the disclosure provides methods of treating orameliorating a symptom of a disease related to TBK1 activity in asubject, e.g., a cell, a tissue, mammal, or human patient, the methodcomprising administering an effective amount of a compound as describedherein or a composition comprising an effective amount of the same andan effective or synergistic amount of another bioactive agent to asubject in need thereof, wherein the composition comprising the same iseffective in treating or ameliorating a symptom of a disease related toTBK1 activity in the subject. In certain embodiments, the disease to betreated is cancer, e.g., prostate cancer, or Kennedy's Disease. In apreferred embodiment, the subject is a human. In certain additionalembodiments, the additional bioactive agent is an anti-cancer agent.

In alternative aspects, the present invention relates to a method fortreating a disease state by degrading a protein or polypeptide throughwhich a disease state or condition is modulated comprising administeringto said patient or subject an effective amount of at least one compoundas described hereinabove, optionally in combination with an additionalbioactive agent. The method according to the present invention may beused to treat a large number of disease states or conditions includingcancer, by virtue of the administration of effective amounts of at leastone compound described herein.

In another aspect, the disclosure provides methods for identifying theeffects of the degradation of proteins of interest in a biologicalsystem using compounds according to the present invention.

Kits

In another aspect, the description provides kits comprising compounds orcompositions as described herein. The kit may be promoted, distributed,or sold as a unit for performing the methods of the present invention.In addition, the kits of the present invention may preferably containinstructions which describe a suitable use. Such kits can beconveniently used, e.g., in clinical settings, to treat patientsexhibiting symptoms of, e.g., cancer or Kennedy's Disease.

Exemplary TBK1 Binding Moieties (TBMs)

TANK-binding kinase 1 (TBK1) is a serine/threonine kinase and anoncanonical member of the IKK family implicated in antiviral immuneresponse as well as tumor genesis and development and is therefore atarget that has attracted considerable attention with regards to theidentification of agents that could diminish its activity. Of particularnote are the various reports regarding the criticality of TBK1 signalingin KRAS mutant tumors, determined using RNAi.

We embarked on a campaign to assess whether TBK1 was degradable by ourtechnology and if so, whether they replicated the KRAS syntheticlethality reported with TBK1 RNAi.

For the design of the TBK1 PROTACs we selected the classic kinaseaminopyridine chemotype 1 as the ligand for TBK1 (K_(d) 1.3 nM), and our4-hydroxyproline derivative 2 as the recruitment ligand for the VonHippel-Lindau (VHL) E3 ligase (IC₅₀ 500 nM FP assay) (FIG. 2).

The PROTAC molecule architecture requires that these ligands beseparated by a connector component (FIG. 2). FIGS. 3 and 4 showsnapshots of the crystal structures of the general VHL and TBK1 ligandchemotypes (PDB codes: 4W9L and 41M0) and suggest points on theseligands where such a connector could be attached that would allow readyegress from the protein in question without obvious detrimental effectson ligand binding. For the TBK1 ligand we selected the para-position ofthe pyrimidine 2-aminophenyl moiety; for the VHL ligand we selected theacetamide moiety as the tethering position.

Not knowing a priori what distance the TBK1 and VHL ligands would haveto be positioned in the PROTAC to effectively associate their respectiveproteins, we undertook a systematic survey of connector length usingflexible and therefore accommodating alkyl ether chemistries (Table 1).

TABLE 1 Effect of connector length on degradation activity # Con- nectorDC₅₀ D_(max) PSA Cmpd Connector atoms (nM) (%) (Å²) 1 NA — >1000 ND 79 2NA — NA NA 112 3

7 >1000 ND 200 4

8 >1000 ND 209 5

9 >1000 ND 200 6

10 >1000 ND 209 7

11 >1000 ND 219 8

12 88 79 209 9

13 71 86 219 10

14 103 92 228 11

15 32 96 219 12

16 95 90 209 13

17 29 96 237 14

18 6 96 228 15

19 25 96 228 16

20 34 96 246 17

21 3 96 237 NA: not applicable. ND: not determined. DC₅₀: concentrationat which 50% degradation is observed. D_(max): maximal degradationobserved. Data represent the mean of ≥2 determinations.

From this initial library, potent, sub-micromolar TBK1-VHL PROTACdegraders were identified (PROTACs 8-17). The gross SAR clearlyindicates a dependence on a minimum connector length with connectors of<12 atoms (ca. 13A in fully extended form) demonstrating no appreciabledegradation activity. Longer connectors appear generally well tolerateddespite their higher PSA and possible cell penetrance burden, and theSAR, to the extent it was explored, indicates no obvious maximumtolerated length. These observations are consistent with the conceptthat the bifunctional PROTAC species mediates the association of theTBK1 and VHL proteins to form a ternary complex, but that a minimumPROTAC length is required to allow the proteins to come together withoutincurring steric conflicts. It was hypothesized that the very flexiblenature of the connector chemistry allows the longer connectors to orientthemselves as necessary to allow the two proteins to associate and forubiquitin to transfer to TBK1. The extent to which the flexibility ofeach individual connector allows it to organize spatially in order toproperly orient the VHL-TBK1 interaction likely governs the efficiencyof such transfer and therefore contributes to the subtle degradation SARseen across PROTACs 8-17, along with differences in cell permeation.

To confirm the mechanistic dependence on VHL for TBK1 degradation, weprepared PROTAC 18, an epimer of active PROTAC 11, which by nature ofthe reversed (S) stereochemistry at the proline 4-position, has noappreciable binding to VHL (FP IC₅₀>5 uM) but is identical in all otherrespects (FIG. 5).

PROTAC 18 showed no significant degradation of TBK1 (FIG. 6), confirmingVHL's role in the degradation of TBK1 by PROTAC 11. It was confirmedthat PROTAC 18 was not significantly compromised in terms of its TBK1binding (Kd 5.9 nM), and also assessed the effect on 11 and 18 on theTBK1 downstream marker pIRF3. Both agents as well as the parent TBK1ligand 1 displayed competent intracellular TBK1 binding as indicated bythe inhibition of pIRF3.

The involvement of the proteasome in the VHL-mediated degradation ofTBK1 by PROTAC 11 was assessed by addition of the proteasome inhibitorcarfilzomib (Kyprolis®) to the assay conditions. Pre-treatment withcarfilzomib markedly reduced the extent of TBK1 degradation by PROTAC 11indicating that the 26S proteasome was indeed implicated in thedegradation of TBK1 (FIG. 7). Also, the addition of excess VHL ligand 2to the assay to compete with PROTAC 11 for VHL, also abrogated TBK1'sdegradation.

With mechanistically specific tool degrader 11 in hand, the impact ofTBK1 binding on degradation potency and efficacy was evaluated. In orderto minimize the impact of any cell permeation or conformationaldifferences on observed degrader potency, only the 5-position of thepyrimidine TBK1 ligand component was modified and only usingfunctionalities that did not substantially alter the 219 Å² polarsurface area of the set (Table 2).

TABLE 2 Effect of TBK1 affinity on degradation activity

Cmpd R₁ TBK1 K_(d) (nM) DC₅₀ (nM) D_(max) (%) 19 H   725 ± 85 >1000 ND20 Cl  10.4 ± 0.6 10 96 21 CF₃ 13 29 96 22 cBu  1035 ± 165 544 70 23 I    4 ± 0.4 3 96 24 F 103.5 ± 6.5 282 74 25 Me   270 ± 40 92 89 26 Et  275 ± 35 121 77 27 Vinyl   130 ± 10 48 96 28 cPr   245 ± 25 65 96 11Br   4.6 ± 1.1 12 96 ND: not determined. DC₅₀: concentration at which50% degradation is observed. D_(max): maximal degradation observed. Datarepresent the mean of ≥2 determinations.

Maximal efficacy (>90% degradation) was achieved with PROTACs that hadTBK1 affinities of ≤245 nM, beyond which degradation begins to drop offalthough remain significant (70%) even in the case of Compound 22 thathas a Kd of 1 μM. That cellular degradation potency shown so high (65nM) given that the affinities for the component ligands of PROTAC 28 toits TBK1 and VHL proteins be so modest (245 and 800 nM, respectively),is likely due to the ability of the PROTAC to initiate multiple cyclesof degradation and drive a process and not an equilibrium mechanism suchas traditional inhibition.

Next, the effect of changing the linker and VHL affinity was evaluatedon degradation (Table 3 and Table 4). PROTACs 11 and 29-33 differ in theside chain chemistry of the glycine component of the VHL ligand which,as for the TBK1 ligand, do not grossly change the molecular propertiesof the PROTACs (PSA 219 Å²) yet do alter their VHL affinity. Maximalefficacy was only seen with the parent PROTAC 11 (R=tBu) although,robust degradation (>70%) was seen with PROTAC 31 (R=Et).

TABLE 3 Effect of VHL affinity on degradation activity

Cmpd R₂ VHL Ligand IC₅₀ (μM) DC₅₀ (nM) D_(max) (%) 29 H 106 >1000 0 30Me 23.6 >1000 34 31 Et 70.4 864 71 32 ^(n)Pr 6.2 288 75 33 ^(i)Pr 1.4544 88 11 ^(t)Bu 0.8 12 96

TABLE 4 Effect of linker and VHL structure on TBK1 degradation % TBK1Com- remaining pound at 1 uM # Structure Cmpd** 34

B 35

C 36

C 37

C 38

C 39

C 40

C 41

C 42

B 43

B 44

B 45

B 46

B 47

B 48

A 49

C 50

C 51

C 52

C 53

C 54

B **A: 0-40% B: 41-80% C: ≥81%

The effect of potent TBK1 degrader, PROTAC 11 was also evaluated on celllines harbouring either wild-type or mutant KRAS. 72 Hour treatment ofKRAS mutant cell lines H23, A549 and H1792, and KRAS wild type cell lineH2110 with PROTAC 11, while effecting near complete degradation of TBK1,caused no differential effect on the proliferation of these cells, thussupporting the literature reports that TBK1 was not synthetically lethalin KRAS mutant versus wild type cells (FIGS. 8A & 8B).^(refs)

Assessment of the affinity of PROTAC 11 to the closely related kinaseIKKε confirmed robust binding with a K_(d) 70 nM. In the case of TBK1this is clearly a sufficient level of affinity for degradation (Table 2,e.g. Compound 27), however interestingly was insufficient for IKKε asnegligible degradation was observed (FIG. 9).

It was hypothesized that this introduction of degradation selectivityinto a relatively unselective ligand may result from a differentialpresentation of TBK1 and its surface lysines to VHL and its reactiveE2-ubiquitin thioester component, as compared to IKKε, and therefore adifferent efficiency of the transfer of ubiquitin to TBK1 (FIG. 1).Other potential explanations include an increased rate ofdeubiquitinylation in the case of IKKε, or that IKKε ubiquitinylationleads to compartmentalization versus degradation in the case of IKKε.

In conclusion, a process for the rapid generation of potent, VHL andproteasome-dependent PROTAC degraders of TBK1, through a systematicsurvey of connector length and ligand affinities has been described. Ithas been also demonstrated that PROTACs can provide greater degradationpotency and selectivity than that anticipated based on the potency andselectivity of the component ligands. In concert with the prevailingliterature opinion, it has been also demonstrated that deletion of TBK1via PROTAC-mediated degradation caused no differential effect on theproliferation between KRAS mutant and KRAS wild type cells.

Assays, Synthetic and Analytical Methods

In vitro degradation assay protocol for compounds 3-33:

Panc02.13 cells were purchased from ATCC and cultured in RPMI-1640(Gibco), supplemented with 15% FBS (ATCC) and 10 Units/mL humanrecombinant insulin (Gibco). PROTAC treatments were carried out in12-well plates for 16 h. TLR3 agonist Poly I:C (Invivogen; tlrl-pic) wasadded for the final 3 h. Cells were harvested, and lysed in RIPA buffer(50 mM Tris pH8, 150 mM NaCl, 1% Tx-100, 0.1% SDS, 0.5% SodiumDeoxycholate) supplemented with protease and phosphatase inhibitors.Lysates were clarified at 16,000 g for 10 minutes, and supernatants wereseparated by SDS-PAGE. Immunoblotting was performed using standardprotocols. The antibodies used were TBK1 (Cell Signaling#3504), pIRF3(abcam#ab76493), and GAPDH (Cell Signaling#5174).

In Vitro Degradation Assay Protocol for Compounds 34-57

MDA MB 231 cells were purchased from ATCC and cultured in RPMI-1640(Gibco), supplemented with 10% FBS (Gibco). PROTAC treatments werecarried out in 24-well plates for 16 h. Cells were harvested, and lysedin RIPA buffer (50 mM Tris pH8, 150 mM NaCl, 1% Tx-100, 0.1% SDS, 0.5%Sodium Deoxycholate) supplemented with protease and phosphataseinhibitors. Lysates were clarified at 16,000 g for 10 minutes, andsupernatants were separated by SDS-PAGE. Immunoblotting was performedusing standard protocols. The antibodies used were TBK1 (CellSignaling#3504) and GAPDH (Cell Signaling#5174).

Representative Experimental Procedure (Compound 11)

1,2-Di(1,3-dioxan-2-yl)ethane

A mixture of 2,5-dimethoxytetrahydrofuran (20 g, 132 mmol),1,3-propanediol (120 g, 1.5 mol) and p-TsOH.H₂O (2.5 g, 15.1 mmol) inDCM (500 mL) was stirred at 40° C. for 16 h. The reaction was quenchedwith 1N NaHCO₃. The organic phase was washed with water, brine, driedover Na₂SO₄, filtered and concentrated. The residue was purified bysilica gel chromatography eluting with 10-30% EtOAc in hexane to afford1,2-di(1,3-dioxan-2-yl)ethane (22.5 g, 74%) as white solid. ¹ HNMR (400MHz, CDCl₃): δ 1.30-1.34 (m, 2H), 1.69-1.70 (m, 4H), 2.01-2.11 (m, 2H),3.71-3.78 (m, 4H), 4.07-4.11 (m, 4H), 4.51-4.55 (m, 2H).

3,3′-(Butane-1,4-diylbis(oxy))bis(propan-1-ol)

To a solution of 1,2-di(1,3-dioxan-2-yl)ethane (22.5 g, 113 mmol) in THF(400 mL) was added BH₃ THF complex (1M, 282 mmol, 282 mL) slowly at 0°C. After the addition, the reaction was stirred at reflux for 48 h. TLCshowed the reaction was complete. MeOH (40 mL) was carefully added intothe reaction mixture at 0° C. and the resulting solution was stirred atroom temperature for additional 2 h. The volatiles were evaporated andthe residue was purified by silica gel chromatography eluting with 6-8%MeOH in DCM to afford 3,3′-(butane-1,4-diylbis(oxy))bis(propan-1-ol)(7.5 g, 32%) as colorless oil. ¹HNMR (400 MHz, CDCl₃): δ 1.62-1.65 (m,4H), 1.79-1.85 (m, 4H), 2.79 (br, 2H), 3.45-3.47 (m, 4H), 3.60 (t, J=6.0Hz, 4H), 3.75 (t, J=5.6 Hz, 4H).

3-(4-(3-(Benzyloxy)propoxy)butoxy)propan-1-ol

To a mixture of 3,3′-(butane-1,4-diylbis(oxy))bis(propan-1-ol) (14 g, 68mmol), Ag₂O (23.6 g, 102 mmol) and KI (4.5 g, 27 mmol) in DCM (120 mL)was added benzyl bromide (12.8 g, 74.7 mmol) dropwise at roomtemperature. The resulting mixture was stirred at room temperature for12 h. The solid was removed by filtration and washed with DCM. Thecombined organic solution was concentrated and the residue was purifiedby silica gel chromatography eluting with 20% EtOAc in hexane to afford3-(4-(3-(benzyloxy)propoxy)butoxy)propan-1-ol (7.8 g, 39%) as colorlessoil. LCMS: 297.3 [M+1]⁺. ¹HNMR (400 MHz, CDCl₃): δ 1.60-1.63 (m, 4H),1.80-1.89 (m, 4H), 2.52 (t, J=5.6 Hz, 1H), 3.40-3.46 (m, 4H), 3.49-3.62(m, 6H), 3.74-3.78 (m, 2H), 4.50 (s, 2H), 7.27-7.34 (m, 5H).

^(t)Butyl 1-phenyl-2,6,11,15-tetraoxaheptadecan-17-oate

To a mixture of 3-(4-(3-(benzyloxy)propoxy)butoxy)propan-1-ol (7.8 g,26.3 mmol) in dry DMF (75 mL) was added NaH (60%, 1.9 g, 47.3 mmol) at0° C. slowly, and the resulting mixture was stirred at room temperaturefor 1.5 h. t-Butyl bromoacetate (12.7 g, 65.8 mmol) was added into thereaction mixture at 0° C. dropwise and the resulting mixture was allowedto stir at room temperature for 15 h. The mixture was carefully quenchedwith water with ice-water cooling and extracted with EtOAc. The organicphase was washed with brine, dried over anhydrous Na₂SO₄, filtered andconcentrated. The residue was purified by silica gel chromatographyeluting with 20-50% EtOAc in hexane to afford the title compound (2.4 g,22%). LCMS: 469.4 [M+1]⁺. ¹HNMR (400 MHz, CDCl₃): δ 1.47 (s, 9H),1.59-1.62 (m, 4H), 1.86-1.91 (m, 4H), 3.40-3.43 (m, 4H), 3.49-3.57 (m,6H), 3.64 (t, J=6.4 Hz, 2H), 4.18 (s, 2H), 4.50 (s, 2H), 4.56 (s, 2H),7.27-7.36 (m, 5H).

^(t)Butyl 2-(3-(4-(3-hydroxypropoxy)butoxy)propoxy)acetate

A solution of tert-butyl 1-phenyl-2,6,11,15-tetraoxaheptadecan-17-oate(2.4 g, 5.1 mmol), Pd/C (10%, 100 mg) in EtOH (50 mL) was stirred atroom temperature 16 h under H₂ atmosphere. Pd/C was removed byfiltration and washed with EtOH. The combined organic phase wasconcentrated to afford the title compound (1.8 g, 93%) as brown oil. Itwas used in next step without further purification.

¹HNMR (400 MHz, CDCl₃): δ 1.48 (s, 9H), 1.62-1.63 (m, 4H), 1.81-1.91 (m,4H), 2.55 (br, 1H), 1.86-1.91 (m, 4H), 3.41-3.47 (m, 4H), 3.51 (t, J=6.4Hz, 2H), 3.60-3.66 (m, 4H), 3.77 (t, J=5.4 Hz, 2H), 4.19 (s, 2H), 4.57(s, 2H).

^(t)Butyl 2-(3-(4-(3-(tosyloxy)propoxy)butoxy)propoxy)acetate

A mixture of tert-butyl 2-(3-(4-(3-hydroxypropoxy)butoxy)propoxy)acetate(800 mg, 2.11 mmol), TsCl (420 mg, 2.54 mmol), TEA (260 mmol, 2.54 mmol)and DMAP (10 mg) in DCM (15 mL) was stirred at room temperature for 8 h.The reaction mixture was diluted with DCM and washed with water andbrine. The organic layer was dried over Na₂SO₄, filtered andconcentrated. The residue was purified by silica gel chromatographyeluting with 10-15% EtOAc in hexane to afford the title compound (850mg, 73%) as colorless oil. LCMS: 533.3[M+1]⁺. ¹HNMR (400 MHz, CDCl₃): δ1.48 (s, 9H), 1.53-1.55 (m, 4H), 1.86-1.92 (m, 4H), 2.45 (s, 3H),3.31-3.34 (m, 2H), 3.39-3.43 (m, 4H), 3.50 (t, J=6.2 Hz, 2H), 3.64 (t,J=6.4 Hz, 2H), 4.13 (t, J=6.2 Hz, 2H), 4.18 (s, 2H), 4.57 (s, 2H), 7.34(d, J=8.0 Hz, 2H), 7.80 (d, J=8.4 Hz, 2H).

^(t)Butyl 2-(3-(4-(3-(4-nitrophenoxy)propoxy)butoxy)propoxy)acetate

A mixture of tert-butyl2-(3-(4-(3-(tosyloxy)propoxy)butoxy)propoxy)acetate (850 mg, 1.6 mmol),K₂CO3 (552 mg, 4 mmol) and 4-nitrophenol (244 mg, 1.76 mmol) in DMF (5mL) was stirred at 70° C. for 16 h. The mixture was partitioned betweenEtOAc and water. The organic phase was washed with brine, dried overanhydrous Na₂SO₄, filtered and concentrated. The residue was purified bysilica gel chromatography eluting with 20-50% EtOAc in hexane to affordthe title compound (650 mg, 81%) as light yellow solid. ¹H NMR (400 MHz,CDCl₃): δ 1.47 (s, 9H), 1.61-1.63 (m, 4H), 1.85-1.91 (m, 2H), 2.06-2.09(m, 2H), 3.41-3.52 (m, 6H), 3.57-3.65 (m, 4H), 4.18 (s, 2H), 4.57 (s,2H), 6.96 (d, J=9.2 Hz, 2H), 8.20 (d, J=9.2 Hz, 2H).

^(t)Butyl 2-(3-(4-(3-(4-aminophenoxy)propoxy)butoxy)propoxy)acetate

A solution of tert-butyl2-(3-(4-(3-(4-nitrophenoxy)propoxy)butoxy)propoxy)acetate (200 mg, 0.4mmol), Pd/C (10%, 20 mg) in EtOH (20 mL) was stirred at room temperatureunder H₂ atmosphere. Pd/C was removed by filtration and washed withEtOH. The combined organic phase was concentrated to afford the titlecompound (120 mg, 64%) as brown oil. The crude product was used directlywithout purification. ¹H NMR (400 MHz, CDCl₃): δ 1.47 (s, 9H), 1.56-1.63(m, 4H), 1.87-1.90 (m, 2H), 1.97-2.03 (m, 2H), 3.40-3.45 (m, 4H), 3.50(t, J=6.4 Hz, 2H), 3.57 (t, J=6.2 Hz, 2H), 3.64 (t, J=6.4 Hz, 2H), 3.98(t, J=6.4 Hz, 2H), 4.18 (s, 2H), 4.57 (s, 2H), 6.64 (d, J=8.8 Hz, 2H),6.74 (d, J=8.8 Hz, 2H).

^(t)Butyl2-(3-(4-(3-(4-((5-bromo-4-((3-(N-methylcyclobutanecarboxamido)-propyl)-amino)pyrimidin-2-yl)amino)phenoxy)propoxy)butoxy)propoxy)acetate

A mixture of tert-butyl2-(3-(4-(3-(4-aminophenoxy)propoxy)butoxy)propoxy)acetate (120 mg, 0.26mmol),N-[3-[(5-bromo-2-chloropyrimidin-4-yl)amino]propyl]-N-methylcyclobutanecarboxamide(96 mg. 0.26 mmol) and TsOH H₂O (23 mg, 0.12 mmol) in dioxane (3 mL) wasstirred at 100° C. for 16 h. The reaction mixture was cooled to roomtemperature, and partitioned between EtOAc and 1N NaHCO₃. The organicphase was washed with water, brine, dried over anhydrous Na₂SO₄,concentrated. The residue was purified by silica gel chromatographyeluting with 2%-5% MeOH in DCM to afford the title compound (120 mg,58%) as yellow oil. LCMS: 796.3 [M+1]⁺.

2-(3-(4-(3-(4-((5-Bromo-4-((3-(N-methylcyclobutanecarboxamido)-propyl)amino)pyrimidin-2-yl)amino)phenoxy)propoxy)butoxy)propoxy)aceticAcid

A mixture of tert-butyl2-(3-(4-(3-(4-((5-bromo-4-((3-(N-methylcyclobutanecarboxamido)-propyl)amino)pyrimidin-2-yl)amino)phenoxy)propoxy)butoxy)propoxy)acetate(120 mg, 0.15 mmol) and LiOH H₂O (17 mg, 0.4 mmol) in THF (2 mL) andwater (0.5 mL) was stirred at room temperature for 2 h. TLC showed thereaction was complete. The reaction mixture was acidified to pH 3-4 with1M HCl, and the mixture was extracted with DCM, dried over anhydrousNa₂SO₄, filtered and concentrated to afford the title compound (100 mg,98%) as yellow oil which was used in the next step without furtherpurification. LCMS: 682.3 [M+1]⁺.

(2S,4R)-1-((S)-18-(4-((5-Bromo-4-((3-(N-methylcyclobutanecarboxamido)-propyl)amino)pyrimidin-2-yl)amino)phenoxy)-2-(tert-butyl)-4-oxo-6,10,15-trioxa-3-azaoctadecan-1-oyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide

To a mixture of2-(3-(4-(3-(4-((5-bromo-4-((3-(N-methylcyclobutanecarboxamido)-propyl)amino)pyrimidin-2-yl)amino)phenoxy)propoxy)butoxy)propoxy)aceticacid (100 mg, 0.147 mmol),(2S,4R)-1-((S)-2-amino-3,3-dimethylbutanoyl)-4-hydroxy-N-((S)-1-(4-(4-methylthiazol-5-yl)phenyl)ethyl)pyrrolidine-2-carboxamidehydrochloride (68 mg, 0.147 mmol), and DIPEA (77 mg, 0.6 mmol) in dryDMF (3 mL) was added HATU (114 mg, 0.3 mmol) at 0° C. The resultingmixture was allowed to stir at room temperature for 0.5 h. TLC showedthe reaction was complete. The mixture was partitioned between EtOAc andwater. The organic phase was washed with water, brine and dried overanhydrous Na₂SO₄, filtered and concentrated. The residue was purified bypreparative TLC to afford the title compound as white solid (22.5 mg,15%). LCMS: 1094.4 [M+1]⁺. ¹H NMR (400 MHz, CD₃OD): δ 1.05 (s, 9H),1.60-1.64 (m, 4H), 1.80-2.26 (m, 15H), 2.48 (s, 3H), 2.86-2.91 (m, 3H),3.26-3.28 (m, 1H), 3.40-3.54 (m, 9H), 3.59-3.64 (m, 4H), 3.83-3.88 (m,2H), 3.97-4.06 (m, 4H), 4.34-4.38 (m, 1H), 4.52-4.61 (m, 3H), 4.71-4.72(m, 1H), 6.87-6.90 (m, 2H), 7.41-7.49 (m, 6H), 7.87-7.90 (m, 1H), 8.88(s, 1H).

N-[3-[(5-Bromo-2-chloropyrimidin-4-yl)amino]propyl]-N-methylcyclobutanecarboxamide

^(t)Butyl N-[3-(1-cyclobutyl-N-methylformamido)propyl]carbamate

Into a 250-mL round-bottom flask purged and maintained with an inertatmosphere of nitrogen, was placed a solution of cyclobutanecarboxylicacid (2.66 g, 26.6 mmol, 1.00 equiv) in N,N-dimethylformamide (100 mL),and DIEA (6.86 g, 53.1 mmol, 2.00 equiv). This was followed by theaddition of HATU (12.13 g, 31.9 mmol, 1.20 equiv). The mixture wasstirred for 30 min at 0-10° C. To this was added tert-butylN-[3-(methylamino)propyl]carbamate (5 g, 26.6 mmol, 1.00 equiv). Theresulting solution was stirred for 12 h at room temperature. Thereaction was then quenched by the addition of 500 mL of water. Theresulting solution was extracted with 3×100 mL of ethyl acetate and theorganic layers combined. The extracts were washed with 1×100 mL of waterand 1×100 mL of brine. The mixture was dried over anhydrous sodiumsulfate and concentrated in vacuo. The residue was purified by silicagel chromatography eluting with ethyl acetate/petroleum ether (1:1).This resulted in 5.9 g (82%) of tert-butylN-[3-(1-cyclobutyl-N-methylformamido)propyl]carbamate as colorless oil.LC-MS (ES⁺): m/z 271.05[MH⁺], t_(R)=0.98 min.

N-(3-Aminopropyl)-N-methylcyclobutanecarboxamide Hydrochloride

Into a 250-mL round-bottom flask, was placed a solution of tert-butylN-[3-(1-cyclobutyl-N-methylformamido)propyl]carbamate (13 g, 48.1 mmol,1.00 equiv) in methanol/HCl (g) (200 mL). The resulting solution wasstirred for 1 h at room temperature. The resulting mixture wasconcentrated under vacuum. This resulted in 9.6 g (97%) ofN-(3-aminopropyl)-N-methylcyclobutanecarboxamide hydrochloride as awhite solid. LC-MS (ES⁺): m/z 171.00 [MH⁺], t_(R)=0.34 min.

N-[3-[(5-Bromo-2-chloropyrimidin-4-yl)amino]propyl]-N-methylcyclobutanecarboxamide

Into a 500-mL 3-necked round-bottom flask purged and maintained with aninert atmosphere of nitrogen, was placed a solution of5-bromo-2,4-dichloropyrimidine (10.55 g, 46.3 mmol, 1.00 equiv) in CH₃CN(250 mL). This solution was cooled to 0° C. and treated with dropwiseDIEA (18 g, 139.3 mmol, 3.00 equiv) and thenN-(3-aminopropyl)-N-methylcyclobutanecarboxamide hydrochloride (9.6 g,46.4 mmol, 1.00 equiv) batchwise. The resulting solution was stirred for3 h at room temperature then quenched by the addition of 50 mL of water.The CH₃CN was removed in vacuo and the resulting solution furtherdiluted with 100 mL of water. This mixture was extracted with 3×100 mLof ethyl acetate and the organic layers combined, washed with 1×100 mLof brine and dried over anhydrous sodium sulfate, and concentrated invacuo. The resulting residue was washed with 2×100 mL of ethylacetate/petroleum ether (1/5) and the solids collected by filtration.This resulted in 11.3 g (67%) ofN-[3-[(5-bromo-2-chloropyrimidin-4-yl)amino]propyl]-N-methylcyclobutanecarboxamideas a white solid. ¹H NMR (400 MHz, CDCl₃) δ 8.09 (s, 1H), 7.20 (b, 1H),3.49-3.47 (m, 4H), 3.46-3.28 (m, 2H), 2.41-2.31 (m, 2H), 2.24-2.16 (m,2H), 2.05-1.80 (m, 2H), 1.80-1.70 (m, 2H); LC-MS (ES⁺): m/z 362.90,364.90 [MH⁺], t_(R)=2.85 min.

Analytical Characterization of TBK1 Compounds:

Compound # MH+ (1) MH+ (2) 7 1038.37 1040.37 34 1054.35 1056.35 161170.46 1172.46 3 978.37  980.37 35 1098.39 1100.39 36 1142.41 1144.4237 1230.47 1232.47 4 994.36  996.36 13 1126.44 1128.44 38 1186.441188.44 39 1038.36 1040.37 40 1110.51 1112.51 6 1022.47 1024.47 111094.53 1096.54 5 1006.46 1008.46 8 1050.49 1052.49 41 1082.46 1084.4642 1200.52 1202.53 10 1082.48 1084.48 43 1068.45 1070.45 44 1154.531156.53 45 1214.55 1216.55 9 1066.50 1068.50 12 1106.57 1108.57 141138.56 1140.56 17 1182.59 1184.59 46 1126.50 1128.51 15 1152.57 1154.5847 1168.57 1170.57 48 1242.61 1244.61 49 1094.45 1096.46 50 1028.57 — 511054.58 — 28 1054.58 — 25 1028.56 — 26 1042.58 — 52 1042.58 — 27 1040.56— 53 1041.06 — 54 1040.56 — 18 1094.43 1096.44 19 1014.52 — 20 1048.421050.42 21 1082.42 — 24 1032.43 — 23 1140.33 — 22 1068.47 — 29 1038.271040.28 30 1052.29 1054.29 31 1066.30 1068.30 32 1080.32 1082.32 331080.32 1082.32 55 1210.41 1212.41 56 1238.44 1240.44 57 1294.50 1296.50

Method to synthesize novel bifunctional molecules, which contains a TBK1recruiting moiety and an E3 Ligase recruiting moiety, through PROTACtechnology is described. PROTAC mediated protein degradation provides apromising strategy in targeting the “undruggable” pathological proteinsby traditional approaches.

As described herein, in one aspect the disclosure provides bifunctionalcompounds comprising the chemical structure: TBM-L-ULM, wherein TBM is aTBK1 binding moiety; L is absent (a bond) or a chemical linker; and ULMis an E3 ubiquitin ligase binding moiety.

In any of the aspects or embodiments described herein, the TBM has thestructure:

Wherein the TBM is covalently coupled to an ULM via an L group.

In any of the aspects or embodiments described herein, the ULM is amoiety that binds an E3 ubiquitin ligase selected from the groupconsisting of Von Hippel-Lindau (VHL) E3 ubiquitin ligase, IAP,cereblon, and MDM2 as described herein.

In any of the aspects or embodiments described herein, the bifunctionalcompound comprise a linker (L) group having the structure: -A_(1 . . .)A_(q)-, wherein A₁ is coupled to the ULM and TBM moiety; and q is aninteger greater than or equal to 0.

In any of the aspects or embodiments described herein, each A unit(i.e., A₁ to A_(q)) is each independently, a bond, CR^(L1)R^(L2), O, S,SO, SO₂, NR^(L3), SO₂NR^(L3), SONR^(L3), CONR^(L3), NR^(L3)CONR^(L4),NR^(L3)SO₂NR^(L4), CO, CR^(L1)═CR^(L2), C≡C, SiR^(L1)R^(L2), P(O)R^(L3),P(O)OR^(L3), NR^(L3)C(═NCN)NR^(L4), NR^(L3)C(═NCN),NR^(L3)C(═CNO₂)NR^(L4), C₃₋₁₁cycloalkyl optionally substituted with 0-6R^(L1) and/or R^(L2) groups, C₃₋₁₁heteocyclyl optionally substitutedwith 0-6 R^(L1) and/or R^(L2) groups, aryl optionally substituted with0-6 R^(L1) and/or R^(L2) groups, heteroaryl optionally substituted with0-6 R^(L1) and/or R^(L2) groups, wherein R^(L1) or R^(L2), eachindependently, can be linked to other A groups to form cycloalkyl and/orheterocyclyl moeity which can be further substituted with 0-4 R^(L5)groups; and wherein R^(L1), R^(L2), R^(L3), R^(L4) and R^(L5) are, eachindependently, H, halo, C₁₋₈alkyl, OC₁₋₈alkyl, SC₁₋₈alkyl, NHC₁₋₈alkyl,N(C₁₋₈alkyl)₂, C₃₋₁₁cycloalkyl, aryl, heteroaryl, C₃₋₁₁heterocyclyl,OC₁₋₈cycloalkyl, SC₁₋₈cycloalkyl, NHC₁₋₈cycloalkyl, N(C₁₋₈cycloalkyl)₂,N(C₁₋₈cycloalkyl)(C₁₋₈alkyl), OH, NH₂, SH, SO₂C₁₋₈alkyl,P(O)(OC₁₋₈alkyl)(C₁₋₈alkyl), P(O)(OC₁₋₈alkyl)₂, CC—C₁₋₈alkyl, CCH,CH═CH(C₁₋₈alkyl), C(C₁₋₈alkyl)═CH(C₁₋₈alkyl),C(C₁₋₈alkyl)═C(C₁₋₈alkyl)₂, Si(OH)₃, Si(C₁₋₈alkyl)₃, Si(OH)(C₁₋₈alkyl)₂,COC₁₋₈alkyl, CO₂H, halogen, CN, CF₃, CHF₂, CH₂F, NO₂, SF₅,SO₂NHC₁₋₈alkyl, SO₂N(C₁₋₈alkyl)₂, SONHC₁₋₈alkyl, SON(C₁₋₈alkyl)₂,CONHC₁₋₈alkyl, CON(C₁₋₈alkyl)₂, N(C₁₋₈alkyl)CONH(C₁₋₈alkyl),N(C₁₋₈alkyl)CON(C₁₋₈alkyl)₂, NHCONH(C₁₋₈alkyl), NHCON(C₁₋₈alkyl)₂,NHCONH₂, N(C₁₋₈alkyl)SO₂NH(C₁₋₈alkyl), N(C₁₋₈alkyl) SO₂N(C₁₋₈alkyl)₂, NHSO₂NH(C₁₋₈alkyl), NH SO₂N(C₁₋₈alkyl)₂, or NH SO₂NH₂.

In any of the aspects or embodiments described herein, the linker (L) isselected from the group consisting of:

In an additional aspect, the disclosure provides compositions comprisingan effective amount of the bifunctional compound as described herein,and a pharmaceutically acceptable carrier.

In any of the aspects or embodiments described herein, the compositioncan further comprise at least one additional bioactive agent. In any ofthe aspects or embodiments described herein, the bioactive agent is ananti-cancer agent. In any of the aspects or embodiments describedherein, the additional anti-cancer agent is selected from the groupconsisting of: everolimus, trabectedin, abraxane, TLK 286, AV-299,DN-101, pazopanib, GSK690693, RTA 744, ON 0910.Na, AZD 6244(ARRY-142886), AMN-107, TKI-258, GSK461364, AZD 1152, enzastaurin,vandetanib, ARQ-197, MK-0457, MLN8054, PHA-739358, R-763, AT-9263, aFLT-3 inhibitor, an androgen receptor inhibitor, a VEGFR inhibitor, anEGFR TK inhibitor, an aurora kinase inhibitor, a PIK-1 modulator, aBcl-2 inhibitor, an HDAC inhbitor, a c-MET inhibitor, a PARP inhibitor,a Cdk inhibitor, an EGFR TK inhibitor, an IGFR-TK inhibitor, an anti-HGFantibody, a PI3 kinase inhibitors, an AKT inhibitor, a JAK/STATinhibitor, a checkpoint-1 or 2 inhibitor, a focal adhesion kinaseinhibitor, a Map kinase kinase (mek) inhibitor, a VEGF trap antibody,pemetrexed, erlotinib, dasatanib, nilotinib, decatanib, panitumumab,amrubicin, oregovomab, Lep-etu, nolatrexed, azd2171, batabulin,ofatumumab, zanolimumab, edotecarin, tetrandrine, rubitecan,tesmilifene, oblimersen, ticilimumab, ipilimumab, gossypol, Bio 111,131-I-TM-601, ALT-110, BIO 140, CC 8490, cilengitide, gimatecan,IL13-PE38QQR, INO 1001, IPdR₁ KRX-0402, lucanthone, LY317615, neuradiab,vitespan, Rta 744, Sdx 102, talampanel, atrasentan, Xr 311, romidepsin,ADS-100380, sunitinib, 5-fluorouracil, vorinostat, etoposide,gemcitabine, doxorubicin, liposomal doxorubicin,5′-deoxy-5-fluorouridine, vincristine, temozolomide, ZK-304709,seliciclib; PD0325901, AZD-6244, capecitabine, L-Glutamic acid,N-[4-[2-(2-amino-4,7-dihydro-4-oxo-1H—pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl]-, disodium salt,heptahydrate, camptothecin, PEG-labeled irinotecan, tamoxifen,toremifene citrate, anastrazole, exemestane, letrozole,DES(diethylstilbestrol), estradiol, estrogen, conjugated estrogen,bevacizumab, IMC-1C11, CHIR-258);3-[5-(methylsulfonylpiperadinemethyl)-indolylj-quinolone, vatalanib,AG-013736, AVE-0005, the acetate salt of [D-Ser(But) 6,Azgly 10](pyro-Glu-His-Trp-Ser-Tyr-D-Ser(But)-Leu-Arg-Pro-Azgly-NH 2 acetate[C₅₉H₈₄N₁₈Oi₄-(C₂H₄O₂)_(x) where x=1 to 2.4], goserelin acetate,leuprolide acetate, triptorelin pamoate, medroxyprogesterone acetate,hydroxyprogesterone caproate, megestrol acetate, raloxifene,bicalutamide, flutamide, nilutamide, megestrol acetate, CP-724714;TAK-165, HKI-272, erlotinib, lapatanib, canertinib, ABX-EGF antibody,erbitux, EKB-569, PKI-166, GW-572016, Ionafarnib, BMS-214662,tipifarnib; amifostine, NVP-LAQ824, suberoyl analide hydroxamic acid,valproic acid, trichostatin A, FK-228, SU11248, sorafenib, KRN951,aminoglutethimide, arnsacrine, anagrelide, L-asparaginase, BacillusCalmette-Guerin (BCG) vaccine, adriamycin, bleomycin, buserelin,busulfan, carboplatin, carmustine, chlorambucil, cisplatin, cladribine,clodronate, cyproterone, cytarabine, dacarbazine, dactinomycin,daunorubicin, diethylstilbestrol, epirubicin, fludarabine,fludrocortisone, fluoxymesterone, flutamide, gleevec, gemcitabine,hydroxyurea, idarubicin, ifosfamide, imatinib, leuprolide, levamisole,lomustine, mechlorethamine, melphalan, 6-mercaptopurine, mesna,methotrexate, mitomycin, mitotane, mitoxantrone, nilutamide, octreotide,oxaliplatin, pamidronate, pentostatin, plicamycin, porfimer,procarbazine, raltitrexed, rituximab, streptozocin, teniposide,testosterone, thalidomide, thioguanine, thiotepa, tretinoin, vindesine,13-cis-retinoic acid, phenylalanine mustard, uracil mustard,estramustine, altretamine, floxuridine, 5-deooxyuridine, cytosinearabinoside, 6-mecaptopurine, deoxycoformycin, calcitriol, valrubicin,mithramycin, vinblastine, vinorelbine, topotecan, razoxin, marimastat,COL-3, neovastat, BMS-275291, squalamine, endostatin, SU5416, SU6668,EMD121974, interleukin-12, IM862, angiostatin, vitaxin, droloxifene,idoxyfene, spironolactone, finasteride, cimitidine, trastuzumab,denileukin diftitox,gefitinib, bortezimib, paclitaxel, cremophor-freepaclitaxel, docetaxel, epithilone B, BMS-247550, BMS-310705,droloxifene, 4-hydroxytamoxifen, pipendoxifene, ERA-923, arzoxifene,fulvestrant, acolbifene, lasofoxifene, idoxifene, TSE-424, HMR-3339,ZK186619, topotecan, PTK787/ZK 222584, VX-745, PD 184352, rapamycin,40-O-(2-hydroxyethyl)-rapamycin, temsirolimus, AP-23573, RAD001,ABT-578, BC-210, LY294002, LY292223, LY292696, LY293684, LY293646,wortmannin, ZM336372, L-779,450, PEG-filgrastim, darbepoetin,erythropoietin, granulocyte colony-stimulating factor, zolendronate,prednisone, cetuximab, granulocyte macrophage colony-stimulating factor,histrelin, pegylated interferon alfa-2a, interferon alfa-2a, pegylatedinterferon alfa-2b, interferon alfa-2b, azacitidine, PEG-L-asparaginase,lenalidomide, gemtuzumab, hydrocortisone, interleukin-11, dexrazoxane,alemtuzumab, all-transretinoic acid, ketoconazole, interleukin-2,megestrol, immune globulin, nitrogen mustard, methylprednisolone,ibritgumomab tiuxetan, androgens, decitabine, hexamethylmelamine,bexarotene, tositumomab, arsenic trioxide, cortisone, editronate,mitotane, cyclosporine, liposomal daunorubicin, Edwina-asparaginase,strontium 89, casopitant, netupitant, an NK-1 receptor antagonist,palonosetron, aprepitant, diphenhydramine, hydroxyzine, metoclopramide,lorazepam, alprazolam, haloperidol, droperidol, dronabinol,dexamethasone, methylprednisolone, prochlorperazine, granisetron,ondansetron, dolasetron, tropisetron, pegfilgrastim, erythropoietin,epoetin alfa, darbepoetin alfa and mixtures thereof.

In any of the aspects or embodiments described herein, the compositioncan comprise an effective amount of at least two different bifunctionalcompounds as described herein.

In any of the aspects or embodiments described herein, the compound asdescribed herein can be selected from the group consisting of:

combinations thereof.

In any of the aspects or embodiments described herein, the disclosureincludes compositions comprising one or more of the above-referencedcompounds, including effective amounts of the same. In any of theaspects or embodiments, the compositions can further include apharmaceutically acceptable carrier.

In an additional aspect, the description provides compositions for usein methods of treating a disease or disorder in a subject comprising thesteps of administering a composition comprising a pharmaceuticallyacceptable carrier and an effective amount of a compound as describedherein to a subject in need thereof, wherein the compound is effectivein treating or ameliorating at least one symptom of the disease ordisorder. In any of the aspects or embodiments, the disease or disorderis at least one of cancer, an inflammatory disease, an autoimmunedisease, septic shock, or viral infection.

The contents of all references, patents, pending patent applications andpublished patents, cited throughout this application are herebyexpressly incorporated by reference.

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims. It is understoodthat the detailed examples and embodiments described herein are given byway of example for illustrative purposes only, and are in no wayconsidered to be limiting to the invention. Various modifications orchanges in light thereof will be suggested to persons skilled in the artand are included within the spirit and purview of this application andare considered within the scope of the appended claims. For example, therelative quantities of the ingredients may be varied to optimize thedesired effects, additional ingredients may be added, and/or similaringredients may be substituted for one or more of the ingredientsdescribed. Additional advantageous features and functionalitiesassociated with the systems, methods, and processes of the presentinvention will be apparent from the appended claims. Moreover, thoseskilled in the art will recognize, or be able to ascertain using no morethan routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

What is claimed is:
 1. A method of treating a disease or disorder in asubject, the method comprising administering a composition comprising abifunctional compound and a pharmaceutically acceptable carrier to asubject in need thereof, wherein the bifunctional compound is effectivein treating or ameliorating at least one symptom of the disease ordisorder and has the chemical structure:TBM-L-ULM, wherein: TBM is a TBK1 binding moiety; L is a bond or achemical linker that covalently couples the TBM and the ULM; and ULM isan E3 ubiquitin ligase binding moiety.
 2. The method of claim 1, whereinthe disease or disorder is at least one of cancer, an inflammatorydisease, an autoimmune disease, septic shock, or a viral infection. 3.The method of claim 1, wherein the TBM structure is represented by:

wherein R₁ is a group selected from Cl, CF₃, cyclobutyl, I, F, methyl,ethyl, vinyl, cyclopropyl, or Br.
 4. The method of claim 1, wherein theTBM has the structure:


5. The method of claim 1, wherein the ULM is a moiety that binds an E3ubiquitin ligase selected from the group consisting of Von Hippel-Lindau(VHL) E3 ubiquitin ligase, IAP, cereblon, and MDM2.
 6. The method ofclaim 1, wherein the chemical linker (L) is a group having thestructure:-(A′)_(q)-, wherein: -(A′)_(q)- is coupled to the ULM and the TBM; and qis an integer greater than or equal to
 0. 7. The method of claim 6,wherein: each A is independently CR^(L1)R^(L2), O, S, SO, SO₂, NR^(L3),SO₂NR^(L3), SONR^(L3), CONR^(L3), NR^(L3)CONR^(L4), NR^(L3)SO₂NR^(L4),CO, CR^(L1)═CR^(L2), C≡C, SiR^(L1)R^(L2), P(O)R^(L1), P(O)OR^(L1),NR^(L3)C(═NCN)NR^(L4), NR^(L3)C(═NCN), NR^(L3)C(═CNO₂)NR^(L4),C₃₋₁₁cycloalkyl optionally substituted with 1-6 R^(L1) and/or R^(L2)groups, C₃₋₁₁heteocyclyl optionally substituted with 1-6 R^(L1) and/orR^(L2) groups, aryl optionally substituted with 1-6 R^(L1) and/or R^(L2)groups, or heteroaryl optionally substituted with 1-6 R^(L1) and/orR^(L2) groups, wherein R^(L1) or R^(L2), each independently, can belinked to other A groups to form cycloalkyl and/or heterocyclyl moietywhich can be further substituted with 1-4 R^(L5) groups; and R^(L1),R^(L2), R^(L3), R^(L4) and R^(L5) are, each independently, H, halogen,C₁₋₈alkyl, OC₁₋₈alkyl, SC₁₋₈alkyl, NHC₁₋₈alkyl, N(C₁₋₈alkyl)₂,C₃₋₁₁cycloalkyl, aryl, heteroaryl, C₃₋₁₁heterocyclyl, OC₃₋₈cycloalkyl,SC₃₋₈cycloalkyl, NHC₃₋₈cycloalkyl, N(C₃₋₈cycloalkyl)₂,N(C₃₋₈cycloalkyl)(C₁₋₈alkyl), OH, NH₂, SH, SO₂C₁₋₈alkyl,P(O)(OC₁₋₈alkyl)(C₁₋₈alkyl), P(O)(OC₁₋₈alkyl)₂, CC—C₁₋₈alkyl, CCH,CH═CH(C₁₋₈alkyl), C(C₁₋₈alkyl)═CH(C₁₋₈alkyl),C(C₁₋₈alkyl)═C(C₁₋₈alkyl)₂, Si(OH)₃, Si(C₁₋₈alkyl)₃, Si(OH)(C₁₋₈alkyl)₂,COC₁₋₈alkyl, CO₂H, halogen, CN, CF₃, CHF₂, CH₂F, NO₂, SF₅,SO₂NHC₁₋₈alkyl, SO₂N(C₁₋₈alkyl)₂, SONHC₁₋₈alkyl, SON(C₁₋₈alkyl)₂,CONHC₁₋₈alkyl, CON(C₁₋₈alkyl)₂, N(C₁₋₈alkyl)CONH(C₁₋₈alkyl),N(C₁₋₈alkyl)CON(C₁₋₈alkyl)₂, NHCONH(C₁₋₈alkyl), NHCON(C₁₋₈alkyl)₂,NHCONH₂, N(C₁₋₈alkyl)SO₂NH(C₁₋₈alkyl), N(C₁₋₈alkyl) SO₂N(C₁₋₈alkyl)₂, NHSO₂NH(C₁₋₈alkyl), NH SO₂N(C₁₋₈alkyl)₂, or NH SO₂NH₂.
 8. The method ofclaim 1, wherein the chemical linker (L) is selected from the groupconsisting of:


9. The method of claim 1, wherein the ULM has the chemical structure:

wherein: the dashed line indicates the attachment of the ULM to thechemical linker group or the TBM; X¹ and X² are each independently abond, O, NR^(Y3), CR^(Y3)R^(Y4), C═O, C═S, SO, or SO₂; R^(Y3) and R^(Y4)are each independently: H; or linear or branched C₁₋₆ alkyl optionallysubstituted by 1 or more halogen or C₁₋₆ alkoxyl; R^(P) is 0, 1, 2, or 3groups in the pyrrolidine moiety, wherein each R^(P) is independently H,halogen, —OH, or C₁₋₃alkyl; W³ is an optionally substituted-T-N(R^(1a)R^(1b)), -T-Aryl, an optionally substituted -T-Heteroaryl, anoptionally substituted -T-Heterocycle, an optionally substituted—NR¹-T-Aryl, an optionally substituted —NR¹-T-Heteroaryl, or anoptionally substituted —NR¹-T-Heterocycle, where T is covalently bondedto X¹; each R¹, R^(1a), and R^(1b) is independently: H; a linear orbranched C₁₋₆ alkyl group optionally substituted by 1 or more halogen or—OH; R^(Y3)C═O; R^(Y3)C═S; R^(Y3)SO; R^(Y3)SO₂; N(R^(Y3)R^(Y4))C═O;N(R^(Y3)R^(Y4))C═S; N(R^(Y3)R^(Y4))SO; or N(R^(Y3)R^(Y4))SO₂; T is anoptionally substituted —(CH₂)_(n)— group, wherein each one of themethylene groups may be optionally substituted with one or twosubstituents, selected from: halogen; a linear or branched C₁-C₆ alkylgroup optionally substituted by 1 or more halogen or OH; or thesidechain of an amino acid, which may be optionally substituted; n is aninteger from 0 to 6; W⁴ is

R_(14a) and R_(14b), is each independently H, haloalkyl, or optionallysubstituted alkyl; W⁵ is a phenyl or a 5-10 membered heteroaryl; and R₁₅is H, halogen, CN, OH, NO₂, N R_(14a)R_(14b), OR_(14a),CONR_(14a)R_(14b), NR_(14a)COR_(14b), SO₂NR_(14a)R_(14b), NR_(14a)SO₂R_(14b), optionally substituted alkyl, optionally substitutedhaloalkyl, optionally substituted haloalkoxy, aryl, heteroaryl,cycloalkyl, cycloheteroalkyl; or

 wherein: R₁₇ is H, halogen, optionally substituted C₃₋₆ cycloalkyl,optionally substituted C₁₋₆ alkyl, optionally substituted C₂₋₆ alkenyl,and C₁₋₆ haloalkyl; and Xa is S or O.
 10. The method of claim 1, whereinthe ULM has the chemical structure:

wherein

indicates the point of attachment to the chemical linker or the TBM. 11.The method of claim 1, wherein the compound has the chemical structure:


12. The method of claim 1, wherein the compound has the chemicalstructure:


13. The method of claim 1, wherein the compound is selected from thegroup consisting of:

and combinations thereof.
 14. The method of claim 1, wherein the ULM hasa chemical structure selected the group consisting of:

wherein: W is independently selected from the group CH₂, CHR, C═O, SO₂,NH, and N-alkyl; X is independently selected from the group absent, O,and S; Y is independently selected from the group NH, N-alkyl, N-aryl,N-hetaryl, N-cycloalkyl, N-heterocyclyl, O, and S; Z is independentlyselected from the group absent, O, and S, except that both X and Zcannot be absent; G and G′ are independently selected from the group H,alkyl, OH, CH₂-heterocyclyl optionally substituted with R′, and benzyloptionally substituted with R′; Q1-Q4 represent a N or a C with a groupindependently selected from H and R; A is independently selected fromthe group H, alkyl, cycloalkyl, Cl, and F; n is an integer from 1-4; Ris: —CONR′R″, —OR′, —NR′R″, —SR′, —SO₂R′, —SO₂NR′R″, —CR′R″—,—CR′NR′R″—, -aryl, -hetaryl, -alkyl, -cycloalkyl, -heterocyclyl,—P(O)(OR′)R″, —P(O)R′R″, —OP(O)(OR′)R″, —OP(O)R′R″, —Cl, —F, —Br, —I,—CF₃, —CN, —NR′SO₂NR′R″, —NR′CONR′R″, —CONR′COR″, —NR′C(═N—CN)NR′R″,—C(═N—CN)NR′R″, —NR′C(═N—CN)R″, —NR′C(═C—NO₂)NR′R″, —SO₂NR′COR″, —NO₂,—CO₂R′, —C(C═N—OR′)R″, —CR′═CR′R″, —CCR′, —S(C═O)(C═N—R′)R″, —SF₅ and—OCF₃, wherein one R is modified to be covalently joined to the chemicallinker (L) or the TBM: R′ and R″ are independently selected from a bond,H, alkyl, cycloalkyl, aryl, hetaryl, and heterocyclyl; and

represents a bond that may be stereospecific ((R) or (S)) ornon-stereospecific.
 15. The method of claim 1, wherein the compositionfurther comprises at least one additional bioactive agent.
 16. Themethod of claim 15, wherein the bioactive agent is an anti-cancer agent.17. The method of claim 15, wherein the bioactive agent is at least oneanti-cancer agent selected from selected from the group consisting of:everolimus, trabectedin, abraxane, TLK 286, AV-299, DN-101, pazopanib,GSK690693, RTA 744, ON 0910.Na, AZD 6244 (ARRY-142886), AMN-107,TKI-258, GSK461364, AZD 1152, enzastaurin, vandetanib, ARQ-197, MK-0457,MLN8054, PHA-739358, R-763, AT-9263, a FLT-3 inhibitor, an androgenreceptor inhibitor, a VEGFR inhibitor, an EGFR TK inhibitor, an aurorakinase inhibitor, a PIK-1 modulator, a Bcl-2 inhibitor, an HDACinhbitor, a c-MET inhibitor, a PARP inhibitor, a Cdk inhibitor, an EGFRTK inhibitor, an IGFR-TK inhibitor, an anti-HGF antibody, a PI3 kinaseinhibitors, an AKT inhibitor, a JAK/STAT inhibitor, a checkpoint-1 or 2inhibitor, a focal adhesion kinase inhibitor, a Map kinase kinase (mek)inhibitor, a VEGF trap antibody, pemetrexed, erlotinib, dasatanib,nilotinib, decatanib, panitumumab, amrubicin, oregovomab, Lep-etu,nolatrexed, azd2171, batabulin, ofatumumab, zanolimumab, edotecarin,tetrandrine, rubitecan, tesmilifene, oblimersen, ticilimumab,ipilimumab, gossypol, Bio 111, 131-TM-601, ALT-110, BIO 140, CC 8490,cilengitide, gimatecan, IL13-PE38QQR, INO 1001, IPdR₁ KRX-0402,lucanthone, LY317615, neuradiab, vitespan, Rta 744, Sdx 102, talampanel,atrasentan, Xr 311, romidepsin, ADS-100380, sunitinib, 5-fluorouracil,vorinostat, etoposide, gemcitabine, doxorubicin, liposomal doxorubicin,5′-deoxy-5-fluorouridine, vincristine, temozolomide, ZK-304709,seliciclib; PD0325901, AZD-6244, capecitabine, L-Glutamic acid,N-[4-[2-(2-amino-4,7-dihydro-4-oxo-1H—pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl]-, disodium salt,heptahydrate, camptothecin, PEG-labeled irinotecan, tamoxifen,toremifene citrate, anastrazole, exemestane, letrozole,DES(diethylstilbestrol), estradiol, estrogen, conjugated estrogen,bevacizumab, IMC-1C11, CHIR-258);3-[5-(methylsulfonylpiperadinemethyl)-indolylj-quinolone, vatalanib,AG-013736, AVE-0005, the acetate salt of [D-Ser(But) 6,Azgly 10](pyro-Glu-His-Trp-Ser-Tyr-D-Ser(But)-Leu-Arg-Pro-Azgly-NH 2 acetate[C₅₉H₈₄N₁₈Oi₄-(C₂H₄O₂)_(X) where x=1 to 2.4], goserelin acetate,leuprolide acetate, triptorelin pamoate, medroxyprogesterone acetate,hydroxyprogesterone caproate, megestrol acetate, raloxifene,bicalutamide, flutamide, nilutamide, megestrol acetate, CP-724714;TAK-165, HKI-272, erlotinib, lapatanib, canertinib, ABX-EGF antibody,erbitux, EKB-569, PKI-166, GW-572016, Ionafarnib, BMS-214662,tipifarnib; amifostine, NVP-LAQ824, suberoyl analide hydroxamic acid,valproic acid, trichostatin A, FK-228, SU11248, sorafenib, KRN951,aminoglutethimide, arnsacrine, anagrelide, L-asparaginase, BacillusCalmette-Guerin (BCG) vaccine, adriamycin, bleomycin, buserelin,busulfan, carboplatin, carmustine, chlorambucil, cisplatin, cladribine,clodronate, cyproterone, cytarabine, dacarbazine, dactinomycin,daunorubicin, diethylstilbestrol, epirubicin, fludarabine,fludrocortisone, fluoxymesterone, flutamide, gleevec, gemcitabine,hydroxyurea, idarubicin, ifosfamide, imatinib, leuprolide, levamisole,lomustine, mechlorethamine, melphalan, 6-mercaptopurine, mesna,methotrexate, mitomycin, mitotane, mitoxantrone, nilutamide, octreotide,oxaliplatin, pamidronate, pentostatin, plicamycin, porfimer,procarbazine, raltitrexed, rituximab, streptozocin, teniposide,testosterone, thalidomide, thioguanine, thiotepa, tretinoin, vindesine,13-cis-retinoic acid, phenylalanine mustard, uracil mustard,estramustine, altretamine, floxuridine, 5-deooxyuridine, cytosinearabinoside, 6-mecaptopurine, deoxycoformycin, calcitriol, valrubicin,mithramycin, vinblastine, vinorelbine, topotecan, razoxin, marimastat,COL-3, neovastat, BMS-275291, squalamine, endostatin, SU5416, SU6668,EMD121974, interleukin-12, IM862, angiostatin, vitaxin, droloxifene,idoxyfene, spironolactone, finasteride, cimitidine, trastuzumab,denileukin diftitox,gefitinib, bortezimib, paclitaxel, cremophor-freepaclitaxel, docetaxel, epithilone B, BMS-247550, BMS-310705,droloxifene, 4-hydroxytamoxifen, pipendoxifene, ERA-923, arzoxifene,fulvestrant, acolbifene, lasofoxifene, idoxifene, TSE-424, HMR-3339,ZK186619, topotecan, PTK787/ZK 222584, VX-745, PD 184352, rapamycin,40-O-(2-hydroxyethyl)-rapamycin, temsirolimus, AP-23573, RAD001,ABT-578, BC-210, LY294002, LY292223, LY292696, LY293684, LY293646,wortmannin, ZM336372, L-779,450, PEG-filgrastim, darbepoetin,erythropoietin, granulocyte colony-stimulating factor, zolendronate,prednisone, cetuximab, granulocyte macrophage colony-stimulating factor,histrelin, pegylated interferon alfa-2a, interferon alfa-2a, pegylatedinterferon alfa-2b, interferon alfa-2b, azacitidine, PEG-L-asparaginase,lenalidomide, gemtuzumab, hydrocortisone, interleukin-11, dexrazoxane,alemtuzumab, all-transretinoic acid, ketoconazole, interleukin-2,megestrol, immune globulin, nitrogen mustard, methylprednisolone,ibritgumomab tiuxetan, androgens, decitabine, hexamethylmelamine,bexarotene, tositumomab, arsenic trioxide, cortisone, editronate,mitotane, cyclosporine, liposomal daunorubicin, Edwina-asparaginase,strontium 89, casopitant, netupitant, an NK-1 receptor antagonist,palonosetron, aprepitant, diphenhydramine, hydroxyzine, metoclopramide,lorazepam, alprazolam, haloperidol, droperidol, dronabinol,dexamethasone, methylprednisolone, prochlorperazine, granisetron,ondansetron, dolasetron, tropisetron, pegfilgrastim, erythropoietin,epoetin alfa, darbepoetin alfa and mixtures thereof.
 18. A method oftreating a disease or disorder in a subject, the method comprisingadministering a composition comprising a bifunctional compound and apharmaceutically acceptable carrier to a subject in need thereof,wherein the bifunctional compound is effective in treating orameliorating at least one symptom of the disease or disorder and has thechemical structure:TBM-L-ULM, wherein: TBM includes a means for recruiting TBK1; L is abond or a chemical linker that covalently couples the TBM and the ULM;and ULM includes a means for recruiting an E3 ubiquitin ligase.
 19. Themethod of claim 18, wherein the disease or disorder is at least one ofcancer, an inflammatory disease, an autoimmune disease, septic shock, ora viral infection.